title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=109 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A new species and new generic synonymy in the family Vietnamellidae (Insecta: Ephemeroptera) from mid-Cretaceous Burmese amber with notes on ancient dispersal across East Gondwana link: https://peerj.com/articles/19048 last-modified: 2025-03-25 description: The monophyletic mayfly family Vietnamellidae has been introduced for a few extant species from the Indomalayan Realm. All these species belong to the genus Vietnamella and have been described in adult and larval stages. Recently, the fossil genus Burmella was established for male and female imagines of two new species from mid-Cretaceous Burmese amber and assigned to the family Vietnamellidae. In this contribution, we describe another species in the genus Burmella, namely B. inconspicuasp. nov. based on a female imago. It clearly differs from the previously described female of B. clypeata by the absence of an extension of the clypeus and by a different venation in fore and hind wings. Furthermore, we discuss here in detail the systematic position of the monotypic species Burmaheptagenia zhouchangfai originally assigned to the family Heptageniidae and provide arguments for the synonymy of the genus Burmaheptagenia syn. nov. with Burmella. We propose the new combination Burmella zhouchangfaicomb. nov., together with a modified generic diagnosis for the genus Burmella and discuss the adult characters of Vietnamellidae. Systematic placement of the genus Burmella in Vietnamellidae and the phylogenetic position of this family within Ephemerelloidea are discussed. We also consider the geographic origin of the family and the role of the Cretaceous Burma Terrane migration as a key event that facilitated the transfer of Gondwanan fauna to Asia. creator: Roman J. Godunko creator: Nadhira Benhadji creator: Alexander Martynov creator: Zhi-Teng Chen creator: Xuhongyi Zheng creator: Arnold H. Staniczek uri: https://doi.org/10.7717/peerj.19048 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Godunko et al. title: Strain differences between C57Bl/6 and DBA/2 mice (Mus musculus) in delayed matching and nonmatching-to-position tasks: impact of sample responses and delay intervals link: https://peerj.com/articles/19200 last-modified: 2025-03-24 description: BackgroundSpatial working memory is commonly assessed in rodents using delayed matching-to-position (DMTP) and delayed nonmatching-to-position (DNMTP) tasks. Although these tasks are widely used to examine memory function, particularly in relation to delay intervals and response requirements, strain differences in task performance remain underexplored. This study investigates spatial working memory in two widely used mouse strains, C57BL/6 and DBA/2, using these tasks.MethodsMice were trained and tested on the DNMTP task first, followed by the DMTP task. Both tasks were conducted with varying delay intervals and response requirements, allowing for the assessment of spatial working memory across different conditions.ResultsBoth strains acquired the tasks. However, DBA/2 mice exhibited a smaller decline in accuracy with increasing delay intervals in the DNMTP task compared to C57BL/6 mice. DBA/2 mice also demonstrated more stable performance across both tasks, whereas C57BL/6 mice showed a more pronounced accuracy decline in the DNMTP task than in the DMTP task. In addition, enhancing response requirements during sample trials improved performance in DBA/2 mice for both tasks, a trend that was not observed in C57BL/6 mice. These findings suggest that task-specific variables, such as response modality (e.g., lever pressing vs. nose poking) and prior training history, can significantly influence strain performance. Overall, these results emphasize the need for considering strain-specific traits and experimental conditions when interpreting behavioral data, particularly for DBA/2 mice, frequently used as models for hippocampal dysfunction. creator: Kazuhiro Goto uri: https://doi.org/10.7717/peerj.19200 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Goto title: Effect of atrial fibrosis on clot burden score and physicochemical properties of thrombus in patients with ischaemic stroke occurring in non-valvular atrial fibrillation link: https://peerj.com/articles/19173 last-modified: 2025-03-24 description: BackgroundTo investigate the effect of the degree of atrial fibrosis on the clot burden score (CBS) and physicochemical properties in patients with acute ischaemic stroke (AIS) due to non-valvular atrial fibrillation (NVAF).MethodsA total of 117 patients with AIS in NVAF attending the Department of Cardiovascular Medicine and the Cerebrovascular Diagnostic and Treatment Centre between August 2021 and May 2024 were included in the study. Baseline clinical data, biochemical indexes, and imaging data of the patients were collected, and the patients were divided into 93 cases of the CBS (score of 0–6) group and 24 cases of the CBS (score of 7–10) group according to the CBS. CBS (score of 0–6) signifies higher clot burden. The enzyme-linked immunosorbent assay was used to measure the concentration of galactaglutinin-3 (gal-3) and transforming growth factor (TGF-β1) in the serum of the patients, and the PTFV1 were collected by 12-lead electrocardiogram, and the differences in the degree of atrial fibrosis between different groups and the risk factors of CBS (score of 0–6) were analysed. To analyse the effect of atrial fibrosis on the collateral circulation of stroke, the patients were divided into 31 cases with good collateral circulation (grade 3–4) and 86 cases with poor collateral circulation (grade 0–2) according to the digital subtraction angiography (DSA) images. The cerebral thrombus was collected from 60 AIS patients who underwent mechanical thrombectomy. The content of erythrocyte, fibrin/platelets and leukocytes in the thrombus was analysed by Mathew’s scarlet blue staining, and the density of thrombus was measured by computed tomography (CT).ResultsA total of 117 patients were included in this study, and the proportion of hypertensive patients, proportion of chronic atrial fibrillation (CAF), B-type natriuretic peptide (BNP), neutrophil/lymphocyte ratio (NLR), D-dimer, uric acid concentration, proportion of patients with PTFV1 < −0.03 mm s, gal-3, and TGF-β1 were higher in the CBS (score of 0–6) group as compared to the CBS (score of 7–10) group (P-value < 0.05). Hypertension, proportion of CAF, homocysteine, NLR, D-dimer, uric acid, PTFV1 < −0.03 mm s, gal-3, and TGF-β1, were risk factors for the development of high CBS in atrial fibrillation (AF), and hypertension and CAF were the most important factors for the occurrence of AF in the independent risk factors for stroke combined with high clot burden. gal-3 and TGF-β1 were risk factors for poor collateral circulation, atrial fibrosis indexes were not associated with thrombus pathological composition and thrombus density.ConclusionsAtrial fibrosis increases clot burden in patients with AIS due to NVAF but does not significantly correlate with the physicochemical properties and density of the thrombus. creator: Juan Zhao creator: Guangjun Deng creator: Weijing Wang creator: Peng Wang creator: Xinyu Shen creator: Xiaoxiao Yuan creator: Haifei Jiang creator: Zhong-bao Ruan uri: https://doi.org/10.7717/peerj.19173 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhao et al. title: Identification and biological characterization of pathogen causing sooty blotch of Ardisia crispa (Thunb.) A.DC. link: https://peerj.com/articles/19130 last-modified: 2025-03-24 description: Sooty blotch, a primary leaf disease affecting Ardisia crispa (Thunb.) A.DC. (A. crispa, AC), significantly impacts both the yield and quality of this medicinal plant. However, the specific species of pathogenic fungi responsible for this disease and their mechanisms of pathogenesis remain unclear. To elucidate the etiology of sooty blotch, it is essential to investigate effective prevention and treatment methods, and provide a theoretical basis for the effective protection of AC. Initially, the alterations in internal organelles that result in sooty blotch were examined using transmission electron microscopy (TEM) and scanning electron microscopy (SEM). Additionally, differential genes were analyzed using differential display reverse transcriptase-PCR (DDRT-PCR) in both healthy and diseased leaves of AC. Moreover, the pathogenic fungi were separated, purified and identified from leaves infected with sooty blotch of AC, and subsequently, their pathogenicity and biological characteristics were tested. Furthermore, the inhibitory effect of pathogens was measured using the water extract of traditional Chinese medicine, based on the growth rate of the mycelium. The findings indicated that the photosynthesis rate of diseased leaves was slower than that of healthy leaves, as revealed by TEM and SEM analyses. Additionally, DDRT-PCR results demonstrated that the differentially expressed genes primarily included those related to zinc finger proteins, acyl-CoA-transferases, and chloroplasts. The phylogenetic tree and pathogenicity test results showed that the pathogens causing sooty blotch of AC were Annulohypoxylon stygium and Diaporthe angelicae. Microscopic observation revealed that Annulohypoxylon stygium and Diaporthe angelicae exhibited distinct microscopic characteristics, and a pH range of 7–10 along with a subdued light environment were more conducive to the growth of pathogens. Additionally, the water extract of Lonicera fulvotomentosa Hsu et S. C. Cheng and A. crispa (Thunb.) A.DC. had a strong antifungal action on the two pathogens of sooty blotch, and the water extract of Ardisia crenate Sims had a better antifungal action on the Diaportheangelicae. In this study, Annulohypoxylon stygium and Diaportheangelicae were reported as pathogenic fungi causing sooty blotch for the first time, and affected the photosynthesis of AC leaf, and these study provides a theoretical basis for the diagnosis and prevention of A. crispa (Thunb.) A.DC. sooty blotch. creator: Demei Yang creator: Jiangli Luo creator: Ying Zhou creator: Sixuan Zhou creator: Xiongwei Liu creator: Chang Liu uri: https://doi.org/10.7717/peerj.19130 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yang et al. title: Polyunsaturated fatty acids and their endocannabinoid-related metabolites activity at human TRPV1 and TRPA1 ion channels expressed in HEK-293 cells link: https://peerj.com/articles/19125 last-modified: 2025-03-24 description: BackgroundPolyunsaturated fatty acids (PUFAs), particularly Omega-3 (ω-3) and Omega-6 (ω-6) PUFAs, may exert neuroprotective effects via the endocannabinoid system (ECS) and are promoted as brain health supplements. However, despite their potential role in endocannabinoid biosynthesis, the impact of PUFAs on ion channels such as TRPV1 and TRPA1, which are modulated by endocannabinoids, remains incompletely understood. Furthermore, the potential in vitro actions of ω-6 and ω-3 PUFA combined in the ratios available in supplements remains uncertain. Therefore, the objective of this study is to evaluate the functional activity of individual PUFAs, their combination in a specific ratio, and their endocannabinoid-related derivatives on TRPV1 and TRPA1 ion channels.MethodologyWe employed a fluorescent calcium-sensitive dye in HEK-293 Flp-In T-REx cells expressing human TRPV1, TRPA1, or an empty vector to measure changes in intracellular calcium concentration ([Ca]i).ResultsCapsaicin and PUFA derivatives such as docosahexaenoyl ethanolamide (DHEA), γ-linolenoyl ethanolamide (γ-LEA) and anandamide (AEA) stimulate TRPV1 activity directly, whereas eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), γ-linolenic acid (γ-LA), and their 9:3:1 ratio triggered TRPV1 response only after prior exposure to phorbol ester. Cinnamaldehyde and PUFA derivatives such as eicosapentaenoyl ethanolamide (EPEA), DHEA, γ-LEA, 2-arachidonoylglycerol (2-AG), 2-arachidonoylglycerol ether (2-AG ether) and AEA triggered TRPA1 response, with EPA, DHA, γ-LA, and the 9:3:1 ratio showing significant effects at higher concentrations.ConclusionsPUFAs alone and their combined form in 9:3:1 ratio stimulate TRPA1 activity, whereas their metabolites trigger both TRPV1 and TRPA1 response. These findings suggest new avenues to explore for research into potential mechanisms underlying the neurological benefits of PUFAs and their metabolites. creator: Atnaf Abate creator: Marina Santiago creator: Alfonso Garcia-Bennett creator: Mark Connor uri: https://doi.org/10.7717/peerj.19125 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Abate et al. title: Differential effects of multiplex and uniplex affiliative relationships on biomarkers of inflammation link: https://peerj.com/articles/19113 last-modified: 2025-03-24 description: Social relationships profoundly impact health in social species. Much of what we know regarding the impact of affiliative social relationships on health in nonhuman primates (NHPs) has focused on the structure of connections or the quality of relationships. These relationships are often quantified by comparing different types of affiliative behaviors (e.g., contact sitting, grooming, proximity) or pooling affiliative behaviors into an overall measure of affiliation. However, it is unclear how the breadth of affiliative behaviors (e.g., how many different types or which ones) a dyad engages in impact health and fitness outcomes. We used a novel social network approach to quantify the breadth of affiliative relationships based on two behaviors: grooming and sitting in contact. Dyadic relationships were filtered into separate networks depending on whether the pair engaged in multiple affiliative behaviors (multiplex networks) or just one (uniplex networks). Typically, in social network analysis, the edges in the network represent the presence of a single behavior (e.g., grooming) regardless of the presence or absence of other behaviors (e.g., contact sitting, proximity). Therefore, to validate this method, we first compared the overall structure of the standard network for each affiliative behavior: all grooming interactions regardless of contact sitting, and all contact sitting interactions regardless of grooming. We then similarly compared the structure of our filtered multiplex vs. uniplex networks. Results indicated that multiplex networks were more modular, reciprocal, and kin-based while connections in uniplex networks were more strongly associated with social status. These differences were not replicated when comparing networks based on a single behavior alone (i.e., all grooming networks vs. all contact sitting networks). Next, we evaluated whether individual network position in multiplex vs. uniplex (novel approach) or grooming vs. contact sitting (traditional approach) networks differentially impact inflammatory biomarkers in a commonly studied non-human primate model system, the rhesus macaque (Macaca mulatta). Being well connected in multiplex networks (networks where individuals both contact sat and groomed) was associated with lower inflammation (IL-6, TNF-alpha). In contrast, being well connected in uniplex grooming networks (dyad engaged only in grooming and not in contact sitting) was associated with greater inflammation. Altogether, these results suggest that multiplex relationships may function as supportive relationships (e.g., those between kin or strong bonds) that promote health. In contrast, the function of uniplex grooming relationships may be more transactional (e.g., based on social tolerance or social status) and may incur physiological costs. This complexity is important to consider for understanding the mechanisms underlying the association of social relationships on human and animal health. creator: Jessica J. Vandeleest creator: Lauren J. Wooddell creator: Amy C. Nathman creator: Brianne Beisner creator: Brenda McCowan uri: https://doi.org/10.7717/peerj.19113 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Vandeleest et al. title: Serum ferritin associated with atherogenic lipid profiles in a high-altitude living general population link: https://peerj.com/articles/19104 last-modified: 2025-03-24 description: BackgroundSerum ferritin (SF) levels are associated with metabolic syndrome and dyslipidemia. However, the association between SF and atherogenic lipid profiles in high-altitude living populations remains unclear.MethodsIn 2021, a cross-sectional study was conducted on adult Tajik individuals residing in Tashkurgan Tajik Autonomous County (average altitude 3,100 meters). Demographic information and anthropometric measurements were collected in local clinics. Fasting blood samples were analyzed using a Beckman AU-680 Automatic Biochemical analyzer at the biochemical laboratory of Fuwai Hospital. Univariate linear regression analyses were used to explore the association between SF and atherogenic lipid levels. Subgroup analysis was used based on gender and different high-sensitivity C-reactive protein (hs-CRP) and serum amyloid A (SAA) levels. The association between higher SF quartiles and different kinds of dyslipidemia were analyzed by logistic regression.ResultsThere were 1,703 participants in total, among which 866 (50.9%) being men. The mean ages of male and female participants were similar (41.50 vs. 42.38 years; P = 0.224). SF levels were significantly correlated with total cholesterol (TC) (Beta = 0.225, P < 0.001), low-density lipoprotein cholesterol (LDL-C) (Beta = 0.197, P < 0.001), high-density lipoprotein cholesterol (HDL-C) (Beta = −0.218, P < 0.001), triglycerides (TG) (Beta = 0.332, P < 0.001), and small dense LDL-C (sdLDL-C) (Beta = 0.316, P < 0.001), with the exception of lipoprotein (a) (Lp(a)) (Beta = 0.018, P = 0.475). SF was significantly correlated with LDL-C and HDL-C in women, and correlated with TC, TG, and sdLDL-C levels in both men and women in different inflammatory conditions. Elevated SF levels was significantly correlated with high TC (OR: 1.413, 95% CI [1.010–1.978]), high TG (OR: 1.602, 95% CI [1.299–1.976]), and high sdLDL-C (OR: 1.631, 95% CI [1.370–1.942]) in men and high TC (OR: 1.461, 95% CI [1.061–2.014]), high LDL-C (OR: 2.104, 95% CI [1.481–2.990]), low HDL-C (OR: 1.447, 95% CI [1.195–1.752]), high TG (OR: 2.106, 95% CI [1.454–3.050]), and high sdLDL-C (OR: 2.000, 95% CI [1.589–2.516]) in women. After adjusting for potential confounders, elevated SF levels continue to be correlated with high TG in male (OR: 1.382, 95% CI [1.100–1.737]) and female (OR: 1.677, 95% CI [1.070–2.628]) participants. In both young and middle-aged subgroups, the associations between SF and TG, TC, HDL-C, LDL-C, and sdLDL-C were still significant.ConclusionsSF was closely related to atherogenic lipid profiles, especially with regard to TG in high-altitude populations. This association cannot be attributed to its role as an inflammation marker. creator: Menglong Jin creator: Mawusumu Mamute creator: Hebali Shapaermaimaiti creator: Hongyu Ji creator: Zichen Cao creator: Sifu Luo creator: Mayire Abudula creator: Abuduhalike Aigaixi creator: Zhenyan Fu uri: https://doi.org/10.7717/peerj.19104 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jin et al. title: The spatial and temporal evolution of habitat quality and driving factors in nature reserves: a case study of 33 forest ecosystem reserves in Guizhou Province link: https://peerj.com/articles/19098 last-modified: 2025-03-24 description: BackgroundBiodiversity plays a crucial role for humanity, serving as a foundation for human survival and development. Habitat quality serves as a critical indicator for assessing biodiversity and holds significant importance in both theoretical and practical domains. The unique natural geographical environment of Guizhou Province has fostered rich biodiversity and facilitated the establishment of numerous nature reserves, predominantly centered on forest ecosystems. Analyzing the habitat quality of nature reserves and its influencing factors is of great significance for maintaining the regional ecosystem stability, promoting sustainable development, and improving the ecological environment.MethodTherefore, taking the 33 nature reserves of forest ecosystem in Guizhou Province as the study area, we first quantified habitat quality using the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model to analyze changes in the nature reserve from 2000 to 2020. Then, we explored the effects of natural and social factors on the spatiotemporal evolution of habitat quality using the optimal parameters-based geographical detector (OPGD).ResultsForests were identified as the primary land-use type in the study area. However, the nature reserves saw an increase area in cropland, and impervious land by 5,001.39 ha and 102.15 ha; a significant decrease in forests and grasslands; and a slight decrease in watersheds. Rapid urbanization, therefore, negatively affected the overall habitat quality of the reserve. Although there is a declining trend in the habitat quality of the nature reserve, the magnitude of change from 2010 to 2020 (−0.04) is smaller than that from 2000 to 2010 (−0.17), indicating that the management of the reserve has been somewhat effective. In national-level nature reserves, interactions between natural geographic factors and socio-economic factors were greater than interactions between natural geographic factors. Similarly, in local-level nature reserves, interactions between natural geographic factors and socio-economic factors outweighed interactions among social factors.ConclusionThe spatiotemporal variability of habitat quality in the study area was shaped by the combined effects of natural and social factors. The habitat quality of local-level protected areas is, furthermore, more significantly affected by human activities, which are the primary cause of their degradation. creator: Xuemeng Mei creator: Yi Liu creator: Li Yue creator: Mingming Zhang uri: https://doi.org/10.7717/peerj.19098 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mei et al. title: Physiological responses of wild birds to artificial grass during introduction to laboratory housing link: https://peerj.com/articles/19095 last-modified: 2025-03-24 description: Introduction of wild animals to captivity induces chronic stress often leading to weight loss, increases in baseline corticosterone, and increased DNA damage. To mitigate these effects, providing enrichment to the captive environment has been proposed. Yet, studies investigating the physiological effects of captive environment enrichments are rare in wild birds. Here, we test the potential of a single enrichment factor by monitoring weight, baseline corticosterone, and DNA damage in two groups of house sparrows (Passer domesticus) during introduction to captivity: (1) birds in standard laboratory cages with food dishes and (2) birds in cages where food is spread across artificial grass to simulate a more natural foraging environment. After 3 weeks, all birds switched environments for 3 additional weeks. Weight was monitored bi-weekly while baseline corticosterone and DNA damage were measured weekly. Initially, both groups lost significant weight and weight plateaued by about 2 weeks of captivity. However, after switching housing environments, only initially grass-caged birds continued to lose weight. After one week of captivity, grass-caged birds had lower DNA damage compared to standard-caged birds. Over time, standard-caged birds remained unchanged and initially grass-caged birds increased damage after switching housing environments. There were no significant differences in baseline corticosterone across groups or over time. Our findings provide limited support for artificial grass as a substantial enrichment in mitigating the physiological consequences associated with introduction to captivity. Furthermore, given the challenges to husbandry of using artificial grass, the data are insufficiently strong to recommend the use of artificial grass as a stress-reducing enrichment to laboratory housing. creator: Bradley P. Pedro creator: L. Michael Romero uri: https://doi.org/10.7717/peerj.19095 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pedro and Romero title: Isolation and in silico analysis of a new subclass of parasporin 4 from Bacillus thuringiensis coreanensis link: https://peerj.com/articles/19061 last-modified: 2025-03-24 description: BackgroundBacillus thuringiensis (Bt) is a Gram-positive bacterium whose strains have been studied mainly for the control of insect pests, due to the insecticidal capacity of its Cry and Vip proteins. However, recent studies indicate the presence of other proteins with no known insecticidal action. These proteins denominated “parasporins” (PS) have cytotoxic activity and are divided into six classes, namely PS1, PS2, PS3, PS4, PS5, and PS6. Among these, parasporins 4 (PS4) has only one described subclass, present in the Bacillus thuringiensis shandongiensis strain. Given the importance and limited knowledge about the actions of PS4 proteins and the existence of only one described subclass, the present work aimed to characterize the Bacillus thuringiensis coreanensis strain as a potential source of PS4 protein.MethodsA preliminary screening to detect the ps4 gene was conducted in a bank of standard strains and isolates of Bacillus thuringiensis from the Laboratory of Bacterial Genetics and Applied Biotechnology, FCAV/UNESP. The positive strain for this gene had its genomic DNA extracted, the ps4 gene was isolated, cloned and in silico analyses of its sequence were performed. Tools such as Bioedit, BLAST, Clustal Omega, Geneious, IQ-Tree, and iTOL were used in these analyses. For the structural analysis of the PS4 detected, in comparison to the database PS4 (BAD22577), the tools Alphafold2, Pymol, and InterPro were used. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gel analyses allowed the visualization of the inactive and active PS4 protein from the positive strain, after solubilization and activation with Proteinase K.ResultsPrevious screening of Bt standard strains revealed the presence of a partial ps4 gene in Bacillus thuringiensis coreanensis strain. The alignment obtained by the BLAST tool revealed 100% identity between the fragment detected in this work with a hypothetical protein (ANN35810.1) from the genome of that same strain. Considering this, the isolation of the complete gene present in this strain was performed by applying the polymer chain reaction (PCR) technique, using the hypothetical sequence as a basis for the primers elaboration. The in silico analysis of the obtained sequence revealed 92.03% similarity with the ps4 sequence presented in the database (AB180980). Protein modeling studies and comparison of their structures revealed that the B. thuringiensis coreanensis has a new subclass of PS4, denominated PS4Ab1, being an important source of parasporin to be explored in biotechnological applications. creator: Thais N. F. Santos creator: Raquel O. Moreira creator: Jardel D. B. Rodrigues creator: Luis A. C. Rojas creator: Jackson A. M. Souza creator: Janete A. Desidério uri: https://doi.org/10.7717/peerj.19061 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Santos et al.