title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=130 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Enhancing active ingredient biosynthesis in Chinese herbal medicine: biotechnological strategies and molecular mechanisms link: https://peerj.com/articles/18914 last-modified: 2025-02-10 description: BackgroundChinese herbal medicine (CHM) is a fundamental component of traditional Chinese medical practice, offering a rich source of natural remedies with significant therapeutic potential. However, the scarcity of active ingredients and complex extraction procedures present substantial challenges to their widespread clinical application. This review aims to address this gap by exploring the potential of modern biotechnological advancements in enhancing the biosynthesis of these valuable compounds.MethodologyThe study takes a comprehensive approach, delving into the chemical composition of CHM’s active ingredients and elucidating their biosynthetic pathways and molecular regulatory mechanisms. Additionally, it surveys recent progress in extraction methodologies and evaluates engineering strategies aimed at synthetic production. This multifaceted analysis forms the foundation for examining the role of synthetic biology in augmenting CHM’s active ingredient synthesis.ResultsOur examination provides insights into the intricate biosynthetic pathways governing the formation of CHM’s active ingredients, as well as the complex molecular regulatory networks that underlie these processes. Furthermore, the review highlights advancements in extraction techniques, demonstrating their ability to streamline and enhance the isolation of these compounds. Engineering approaches for synthetic production, including metabolic engineering and synthetic biology tools, are assessed for their potential to overcome natural limitations and scale up production.ConclusionsBy integrating insights from biosynthesis, molecular regulation, extraction methodologies, and synthetic biology, this review establishes a robust theoretical framework for enhancing the production of CHM’s active ingredients. The proposed strategies and practical guidance aim to facilitate their broader utilization in modern medicine while promoting sustainability and accessibility within this invaluable medicinal heritage. creator: Ziyi Guo creator: Ning Yang creator: Delin Xu uri: https://doi.org/10.7717/peerj.18914 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Guo et al. title: A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma link: https://peerj.com/articles/18895 last-modified: 2025-02-10 description: BackgroundTumor development involves the critical role of programmed cell death (PCD), but the correlation between colon adenocarcinoma (COAD) and PCD-related genes is not clear.MethodsSubtyping analysis of COAD was performed by consensus clustering based on The Cancer Genome Atlas (TCGA), with the AC-ICAM queue from the cBioportal database as a validation set. Immune infiltration of the samples was evaluated using CIBERSORT and Microenvironment Cell Populations (MCP)-counter algorithms. Patients’ immunotherapy response was predicted by the TIDE and aneuploidy scores. Pathway enrichment analysis was conducted with gene set enrichment analysis (GSEA). A RiskScore model was established with independent prognostic PCD-related genes filtered by Cox regression analysis. The mafCompare function was used to compare the differences in mutation rates of somatic genes. Wound healing, transwell assays and Flow cytometer were applied to measure the cell migration, invasion and apoptosis.ResultsThe patients were grouped into S1 and S2 subtypes based on a total of 21 PCD genes associated with the prognostic outcomes of COAD. Specifically, patients of S1 subtype were mainly related to the pathway activation in tumor invasion and deterioration and had a worse prognosis. A RiskScore model was established based on six prognostic genes, including two protective genes (ATOH1, ZG16) and four risk genes (HSPA1A, SEMA4C, CDKN2A, ARHGAP4). Notably, silencing of CDKN2A inhibited the activity of migration and invasion and promoted apoptosis of tumor cells. Based on the RiskScore model, the patients were grouped into high- and low-risk groups. Independent prognostic factors, namely, Age, pathologic_M, pathologic_stage, and RiskScore, were integrated to develop a nomogram with strong good prediction performance. High-risk group had high-expressed immune checkpoint genes and higher TIDE scores, showing a strong immune escape ability and less active immunotherapy response. Compared to the low-risk group, TP53 exhibited a higher rate of somatic mutation in the high-risk group.ConclusionWe constructed a RiskScore model with six PCD-related genes for the prognostic assessment of COAD, providing a valuable insight into the exploration of new targets for the prognostic improvement in COAD. creator: Lei Zheng creator: Jia Lu creator: Dalu Kong creator: Yang Zhan uri: https://doi.org/10.7717/peerj.18895 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zheng et al. title: Microplastic effects on mouse colon in normal and colitis conditions: A literature review link: https://peerj.com/articles/18880 last-modified: 2025-02-10 description: BackgroundTaking into account the global spread of microplastic (MP) pollution, the problem of the MP impact on human health is relevant. MP enters the organism predominantly with water and food, and is mostly detected in the large intestine. Therefore, the connection between MP pollution and the increase in colitis is an important question. In order to assess the toxic and pathogenetic effects of MP, experimental studies were actively conducted during recent years, mainly on laboratory mice.ObjectivesThe aim of our review was to summarize and systematize the data on the MP effect on mice colon under normal conditions and during colitis in order to assess the role of MP in the development of intestinal diseases. This manuscript could be relevant for ecologists, experimental biologists, and physicians dealing with problems related to anthropogenic environmental changes and inflammatory bowel diseases.Survey MethodologyThe search was conducted based on PubMed data about original experimental studies of the MP effects on the colon of healthy mice and mice with colitis.ResultsIn healthy mice colon, MP can cause oxidative stress, increased permeability, immune cell infiltration, production of proinflammatory factors, and decreased mucus production. MP affects proliferation, apoptosis, and differentiation of epithelial cells, expression of tight junction components and glycocalyx, membrane transport, signaling pathways, metabolome, and intestinal microflora composition. In mice with acute and chronic experimental colitis, MP consumption leads to a more pronounced pathological process course.ConclusionsMP may be one of the factors contributing to the development of colitis in humans. However, further research is needed. creator: Natalia Zolotova creator: Dzhuliia Dzhalilova creator: Ivan Tsvetkov creator: Maria Silina creator: Nikolai Fokichev creator: Olga Makarova uri: https://doi.org/10.7717/peerj.18880 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zolotova et al. title: Nanoparticles modified bioceramic sealers on solubility, antimicrobial efficacy, pushout bond strength and marginal adaptation at apical-third of canal dentin link: https://peerj.com/articles/18840 last-modified: 2025-02-10 description: ObjectiveThe present study investigates the solubility, antimicrobial potency, pushout bond strength (PBS), and marginal adaptation of sealer modified using various nanoparticles (NPs) (silver, chitosan, HapNPs) to the root dentin at the apical third.MethodsForty-four human premolars were prepared for root canal treatment via a chemical mechanical approach. The teeth included were subsequently distributed into four groups based on the type of modified and unmodified sealers. Group 1 bioceramic (BC) sealer (Control), Group 2 (AgNPs modified BC sealer), Group 3 (CHNPs modified BC sealer), and Group 4 (HApNPs modified BC sealer). Solubility was assessed by making five samples and measured via precision balance. Antimicrobial testing against E. faecalis was performed using the Agar diffusion test. The bond strength and failure modes were assessed utilizing a universal testing machine and stereomicroscope respectively. A pair of specimens from each cohort was fixed to an aluminum stub to assess marginal adaptation via SEM at the apical third. Data analysis was performed utilizing one way ANOVA and followed by Tukey’s post hoc test (p < 0.05).ResultsSealers-modified HApNPs exhibited the lowest solubility (3.884 ± 0.15%) and strongest PBS (9.63 ± 0.12 MPa). Group 1 (Control) demonstrated highest solubility rate (6.144 ± 0.39%) and weakest bond strength (6.50 ± 0.09 MPa). All the modified sealers exhibited the largest zone of inhibition with no significant difference. Whereas the unmodified BC sealer group presented the smallest zone of bacterial inhibition.ConclusionMarginal adaptation of sealers does not affect the bond strength outcomes achieved. The incorporation of silver, chitosan, and hydroxyapatite nanoparticles into BC root canal sealers resulted in reduced solubility, enhanced antibacterial efficacy, and improved PBS compared to unmodified BC canal sealers. creator: Basil Almutairi creator: Fahad Alkhudhairy uri: https://doi.org/10.7717/peerj.18840 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Almutairi and Alkhudhairy title: The association between serum lipids at diagnosis and renal outcome in microscopic polyangiitis patients link: https://peerj.com/articles/18839 last-modified: 2025-02-10 description: ObjectivesMicroscopic polyangiitis (MPA) is a subgroup of ANCA-associated vasculitis (AAV), which is characterized by vascular endothelial cell damage caused by abnormally activated neutrophils. Dyslipidemia is associated with vascular endothelial cell injury, and the relationship between blood lipid levels and renal prognosis in MPA patients is not clear. We aim to investigate the correlation between blood lipid levels at diagnosis and renal prognosis in MPA patients.MethodsFirstly, we retrospectively included 110 patients diagnosed with MPA and the primary endpoint was the occurrence of end stage renal disease (ESRD). The association between blood lipids at diagnosis and renal outcome was evaluated with Cox regression analysis and survival analysis. Secondly, we explored the potential underlying mechanism of poor renal prognosis in patients with high triglycerides (TG) levels at diagnosis using data independent acquisition (DIA) quantitative proteomics.ResultsDuring a median follow-up period of 23 months, 44 out of 110 patients (40%) developed ESRD. High serum TG at diagnosis was associated with ESRD development after adjusting for several confounding factors including age, gender, body mass index (BMI), hypertension, diabetes mellitus, estimated glomerular filtration rate (eGFR) and Birmingham Vasculitis Activity Score (BVAS). Serum very low-density lipoprotein (VLDL) demonstrated a marginal trend towards association with ESRD development. MPA patients with TG >1.45 mmol/L or VLDL > 0.66 mmol/L had significantly higher risk of ESRD development than those with TG ≤ 1.45 mmol/L or VLDL ≤ 0.66 mmol/L. DIA quantitative proteomics analysis suggested that patients with elevated TG levels and severe MPA had an upregulation of profibrotic pathways, inflammatory signaling, and complement and coagulation cascades, in contrast to those with lower TG levels and milder disease severity.ConclusionsIn MPA patients, high TG or VLDL at diagnosis is associated with an increased risk of ESRD development. The potential mechanisms may be associated with the upregulation of profibrotic and inflammatory signaling pathways, and the activation of complement and coagulation cascades. creator: Zigui Zheng creator: Yujia Wang creator: Jingzhi Xie creator: Zhimin Chen creator: Bingjing Jiang creator: Yanfang Xu uri: https://doi.org/10.7717/peerj.18839 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zheng et al. title: Genome-wide survey and expression analysis of the OMT gene family in Stephania japonica link: https://peerj.com/articles/18600 last-modified: 2025-02-10 description: BackgroundO-methyltransferase (OMT) is an important rate-limiting enzyme that plays a vital role in synthesizing various key metabolites, such as benzylisoquinoline alkaloids (BIA). Nevertheless, there is a dearth of extensive research on the analysis of the OMT gene family in Stephania japonica, a main source of cepharanthine with an anti-coronavirus effect.MethodsTwo OMT family genes, SjCCoAOMT and SjCOMT, were identified from the high-quality genome of S. japonica during this investigation. Further analysis of SjCCoAOMT and SjCOMT genes involved chromosome distribution, gene structure, phylogenetic relationship, conserved motif, expression profile, quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) experiments an d cis-acting elements analysis.ResultsThere are six SjCCoAOMT members and fifty-two SjCOMT members in the genome of S. japonica, which are unevenly distributed on 11 chromosomes. OMTs could be clustered into SjCCoAOMT and SjCOMT subfamilies through phylogenetic relationship, consistent with the conserved motif and gene structure analysis results. The expression profile revealed SjCOMT11 and SjCOMT13 showed specific expression levels mainly in root. SjCOMT21, SjCOMT33 and SjCOMT37 were significantly expressed in the root and slightly expressed in the stem, bud and leaf. SjCOMT15 and SjCOMT45 were not only significantly expressed in root, but also expressed highly in leaf. Significantly enhanced expression of SjCOMT11, SjCOMT13, SjCOMT15, SjCOMT21, SjCOMT33, SjCOMT37, and SjCOMT45 suggested these OMTs are essential for cepharanthine synthesis in the S. japonica roots. Cis-acting element analysis revealed the potential roles of OMTs in S. japonica in growth, development, and resistance to stress. These findings provide insight into understanding the functions and characterization of OMTs from S. japonica and lay a foundation for further revealing the role of the OMT genes in the biosynthesis of cepharanthine. creator: Zenghao Bi creator: Tianxing He creator: Yuting Liang creator: Changqing Zhou creator: Yuetong Yu creator: Liang Leng uri: https://doi.org/10.7717/peerj.18600 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Bi et al. title: New record of Frilled shark Chlamydoselachus anguineus Garman, 1884 (Chondrichthyes: Hexanchiformes) in the South Pacific Ocean link: https://peerj.com/articles/18992 last-modified: 2025-02-07 description: Frilled sharks are rarely observed and limited information is available regarding their life history. The global number of records for these sharks does not exceed 40, with most sightings reported in the Western Pacific Ocean. In 1976, one specimen was recorded for the first time in the South East Pacific Ocean; however, this study provides new evidence for the presence of Chlamydoselachus anguineus in Chilean waters, extending its distribution range 850 km south of the previous record. The morphological features of all specimens from Chile are discussed, supplementing previous observations and adding to the existing knowledge on this species in the Pacific Ocean. creator: Maria J. Indurain creator: Angel Mancilla creator: Leandro Brizuela creator: Carolina Vargas-Caro creator: Carlos Bustamante uri: https://doi.org/10.7717/peerj.18992 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Indurain et al. title: Berberine-induced browning and energy metabolism: mechanisms and implications link: https://peerj.com/articles/18924 last-modified: 2025-02-07 description: Obesity has become a global pandemic. The approaches researched to prevent it include decreasing energy intake and/or enhancing energy expenditure. Therefore, research on brown adipose tissue is of great importance. Brown adipose tissue is characterized by its high mitochondrial content. Mitochondrial uncoupling protein 1 (UCP1) releases energy as heat instead of chemical energy. Thermogenesis increases energy expenditure. Berberine, a phytochemical widely used in Asian countries, has positive effects on body weight control. While the precise mechanisms behind this effect remain unclear, the adenosine monophosphate-activated protein kinase (AMPK) pathway is known to play a crucial role. Berberine activates AMPK through phosphorylation, significantly impacting brown adipose tissue by enhancing lipolytic activity and increasing the expression of UCP1, peroxisome proliferator-activated receptor γ-co-activator-1α (PGC1α), and PR domain containing 16 (PRDM16). While investigating the mechanism of action of berberine, both the AMPK pathway is being examined in more detail and alternative pathways are being explored. One such pathway is growth differentiation factor 15 (GDF15), known for its appetite-suppressing effect. Berberine’s low stability and bioavailability, which are the main obstacles to its clinical use, have been improved through the development of nanotechnological methods. This review examines the potential mechanisms of berberine on browning and summarizes the methods developed to enhance its effect. creator: Aslıhan Alpaslan Ağaçdiken creator: Zeynep Göktaş uri: https://doi.org/10.7717/peerj.18924 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Alpaslan Ağaçdiken and Göktaş title: Assessing the quality of life among African medical and health science students using the WHOQOL-BREF tool link: https://peerj.com/articles/18809 last-modified: 2025-02-07 description: BackgroundThe quality of life (QoL) among health professional students is available in the literature, yet there is a paucity of information concerning QoL among African students. The study aimed to measure the QoL with the World Health Organization Quality of Life-BREF (WHOQOL-BREF) tool among African medical and health science students.MethodsA cross-sectional study was conducted involving 349 African medical and health science students from various disciplines at the International African University in May 2024. A purposive sampling method was used to recruit participants from five different faculties. Data were collected using the WHOQOL-BREF tool, and analyzed using descriptive statistics, chi-square test and multiple linear regression to determine the predictors of QoL among students.ResultsThe overall QoL among 349 African medical and health science students was moderate, with a mean score of 67.5% ± 10.8%. The highest mean scores were observed in the physical health domain (69.3% ± 12.0%), while the lowest scores were in the environmental domain (62.9% ± 12.0%). The multiple regression analysis using demographic data as predictors of QoL revealed that dentistry students were significant predictors of higher overall QoL scores compared to other student groups (β = 7.059, p < 0.05), as well as specific QoL domains including physical health (β = 6.328), psychological health (β = 8.415), social relationships (β = 7.823), and environment (β = 7.017). Furthermore, students from the fields of laboratory sciences and medicine significantly predicted higher scores in the physical health domain (β = 5.223) and the psychological health domain (β = 4.433), respectively. Age was also a significant predictor; students aged between 20 and 23 years showed a positive impact on social relationship domain of QoL (β = 10.296). However, second year (β = −11.146), third year (β = −13.629), and fourth-year students (β = −10.144) exhibited lower social relationship domain of QoL scores.ConclusionStudents of medical and health sciences in Africa exhibited moderate quality of life (QoL). The findings indicate that dentistry students generally experience higher QoL across multiple domains, which contrasts with students from other disciplines, such as pharmacy and nursing. Age and academic year were also significant predictors of QoL, with younger students and those in their initial years of study reporting lower scores. These results align with existing literature and underscore the need for targeted interventions to support students, particularly those in high-stress disciplines or at earlier stages of their education. creator: Fatima Alzahra Galgam creator: Adil Abdalla creator: Mahmoud Shahin creator: Magda Yousif creator: Nahla Abdulrahman creator: Fatmah Alamoudi creator: Mehrunnisha Ahmad creator: Amira Yahia creator: Mohammad Sidiq creator: Aksh Chahal creator: Fuzail Ahmad creator: Mohammad Abu Shaphe creator: Gopal Nambi creator: Moattar Raza Rizvi creator: Faizan Kashoo uri: https://doi.org/10.7717/peerj.18809 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Galgam et al. title: Effect of intercropping Lolium perenne in Ziziphus jujuba orchards on soil quality in the canopy link: https://peerj.com/articles/18710 last-modified: 2025-02-07 description: The cultivation of Lingwu jujube traditionally employs clean tillage, leaving substantial gaps between rows and exposing almost 60% of the orchard to the elements. This method promotes rapid soil moisture evaporation, exacerbates soil erosion, and deteriorates the soil’s physicochemical properties. Consequently, there is a critical need for a more sustainable planting approach that optimally utilizes land resources. A pertinent question is whether varying densities of ryegrass intercropping can improve the uptake of nutrients and water by the jujube tree, the primary species in this ecosystem. In this context, a 2-year field experiment was conducted with three densities of perennial ryegrass intercropped with Lingwu jujube. The experiment assessed the impact on soil’s physical and chemical attributes beneath the jujube canopy, with a focus on correlating soil moisture, enzyme activity, and physical properties. The findings reveal that intercropping at a medium density most effectively enhanced the soil’s physical characteristics. Relative to monoculture, this approach increased the proportion of water-stable aggregates (0.5–0.25 mm) by 4.16%, decreased the soil’s fractal dimension by 0.46%, augmented the field water holding capacity by 14.78%, and significantly boosted soil enzyme activity. Furthermore, high-density ryegrass intercropping elevated the soil’s organic matter content by 36.09% and ameliorated both the pH and cation exchange capacity. Conversely, low-density intercropping raised soil moisture levels by 40.18% in the top 20 cm of the soil. Collectively, these results suggest that an optimal density of ryegrass in intercropping not only bolsters the moisture retention capabilities of soil in Lingwu jujube orchards but also enhances overall soil fertility. Therefore, the adoption of ryegrass and jujube tree intercropping is highly advisable in the ecologically sensitive and resource-constrained arid sandy regions of northern China, offering substantial practical benefits. creator: Yao Ma creator: Bin Cao creator: Xiaojia Wang creator: Weijun Chen uri: https://doi.org/10.7717/peerj.18710 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ma et al.