Search Results (4,067)

(1) Background: Mammographic breast density (MBD) is a well-established predictor of breast cancer risk, yet the biological mechanisms underlying this association remain incompletely understood. MBD is characterized by alterations in breast stromal architecture, including increased collagen deposition and changes in immune cell composition. Given emerging evidence that the breast harbors a resident microbiome, we investigated whether the breast tissue microbiome correlates with MBD. (2) Methods: Adjacent normal breast tissue was collected under sterile conditions from 33 women undergoing surgery for benign or malignant breast disease. DNA was extracted and subjected to 16S rRNA gene sequencing (Illumina MiSeq). (3) Results: We observed a non-significant trend toward lower α-diversity in high-MBD samples compared to low-MBD samples, p = 0.13. β-Diversity analyses identified a modest association between MBD and microbial community composition (MiRKAT p = 0.049). A random forest-based model incorporating genus-level relative abundances improved prediction of MBD over clinical characteristics alone, identifying Corynebacterium (Actinobacteria) and other genera as key predictors. (4) Conclusions: Breast tissue microbial features vary with mammographic breast density, suggesting a potential association with density-associated breast cancer risk. These exploratory findings warrant validation in larger cohorts to better elucidate biological mechanisms and clinical relevance. Full article

Medicago sativa is one of the world’s most important forage plants, possessing strong nitrogen-fixing and regrowth capabilities. Promoting its growth not only enhances stress resistance but also reduces the use of chemical fertilizers. The value of Centella asiatica is primarily reflected in its medicinal properties. Currently, endophytic fungal resources of C. asiatica are scarce, and their potential to promote medicinal components and the underlying mechanisms remains unclear. This study employed DNA extraction techniques to isolate and identify endophytic fungi from different parts of C. asiatica. We systematically analyzed the plant growth-promoting traits of endophytic fungi. After screening for the optimal strain and inoculating it into Medicago sativa, we elucidated the mechanisms underlying its growth-promoting effect using metabolomic sequencing. Research findings: A total of 18 endophytic fungal strains were isolated, belonging to 12 genera. Among them, five indole-3-acetic acid (IAA) strains were identified, with strain J4 demonstrating the highest IAA production (17.157 mg·L⁻¹). The J4 strain has iron-transporting carrier activity, while 15 strains exhibit nitrogen-fixing activity. Inoculation with the Plectosphaerella plurivora strain significantly increases M. sativa’s germination rate, fresh weight, dry weight, and plant height. Metabolomic analysis indicates that P. plurivora may promote anthocyanin and jasmonic acid accumulation by regulating pathways such as flavonoid biosynthesis and pyrimidine metabolism, thereby promoting growth. This study reveals the mechanism by which endophytic fungi enhance M. sativa growth at the metabolomic level. This study reveals the growth-promoting mechanism of endophytic fungi in M. sativa from a metabolomic perspective, providing a theoretical basis for increasing forage yield and offering new insights into sustainable agricultural development. Full article

Sugar beet (Beta vulgaris L.) is one of the most important sugar crops and potential energy crops in China. The utilization of its heterosis is crucial for breaking through the bottlenecks in yield and quality, while the fertility identification of binary male-sterile lines is the core link to ensure the purity of hybrid seeds. Due to its indeterminate inflorescence, artificial emasculation of sugar beet is not feasible, which significantly increases the difficulty in hybrid seed production. To rapidly and accurately identify the fertility composition of monogerm binary male-sterile lines of sugar beet, ensure the maternal line purity in sugar beet hybrid seed production, and improve breeding efficiency, this study conducted fertility identification using molecular marker technology with 7 monogerm binary male-sterile line germplasm resources (297 plants) provided by three research institutions in different regions of China. Genomic DNA was extracted from young sugar beet leaves by the CTAB method. The cytoplasmic fertility types were identified using the TR1 primer, and the fertility gene composition at the nuclear Rf1 locus was verified by the s17 molecular marker combined with Hap II and Hind III double digestion. The results showed that in the cytoplasmic fertility identification, the proportion of S-type cytoplasm in Lines 2 to 7 reached 100%, indicating stable sterility without maintainer line contamination; Line 1 had 93.33% S-type cytoplasm, mixed with 6.67% N-type cytoplasm. For the nuclear Rf1 locus identification, 93.27% (277 plants) of the tested materials yielded the target 1800 bp band by PCR amplification, which were preliminarily identified as homozygous recessive type. Among them, Lines 1 to 3 all showed a single 1800 bp band pattern, indicating homozygous and consistent nuclear fertility genotypes; 20 plants (6.73%) in Lines 4 to 7 exhibited a composite 1800/1300 bp band pattern, suggesting the presence of restorer allele contamination in some lines. Genotype analysis based on 35 enzyme-digested verification samples revealed that the 4/4 genotype had the highest proportion. This study realized the rapid and accurate identification of cytoplasmic and nuclear fertility in monogerm binary male-sterile lines of sugar beet through molecular marker technology, clarified the fertility purity status of 7 germplasm resources, and verified the application value of this technology in the fertility identification of sugar beet binary male-sterile lines. These results provide a scientific basis and technical support for controlling maternal line purity and improving breeding efficiency in sugar beet hybrid seed production. Full article

Cancer is a major health concern, with its incidence rate continuing to increase. There is growing interest in the microbiota and its role in carcinogenesis, as it significantly influences physiological and pathological processes. Various aspects of the microbiome have been shown to have both anti-tumor and pro-tumor effects. Advances in techniques such as high-throughput DNA sequencing have greatly improved our understanding of microbial populations in the human and canine gut. We aimed to (1) characterize the intestinal microbiota of healthy dogs and dogs with cutaneous mast cell tumors (MCTs), (2) assess changes in the intestinal microbiota of dogs undergoing electrochemotherapy (ECT) combined with gene electrotransfer (GET) of the IL-12 plasmid (IL-12), and (3) explore possible associations with the expression of immune markers Programmed cell death protein 1 (PD-1), Programmed death-ligand 1 (PD-L1), and Granzyme B (GZMB) in MCT tissue. Stool samples were collected from healthy dogs (n = 24) and dogs with MCTs (n = 24) before and after ECT and IL-12 GET. DNA was extracted from the samples, and shallow shotgun sequencing was performed. Immunohistochemistry was performed on the tumors to assess the expression of PD-1, PD-L1, and GZMB. The dysbiosis index, alpha diversity, and beta diversity did not differ between groups. Regarding microbial composition, Bifidobacterium animalis, Corynebacterium variabile, Lactobacillus johnsonii, Pediococcus pentosaceus, Streptococcus anginosus, Streptococcus equinus, Streptococcus intermedius, Clostridium thermobutyricum, Megasphaera elsdenii, and Anaerobiospirillum sp. were found in lower relative abundance in feces of dogs with MCTs, while Bacteroides togonis, Lactobacillus amylolyticus, Prevotella sp. CAG:279, and Megamonas hypermegale were more abundant compared to healthy dogs. Our study provides further insight into the composition of the gut microbiota in dogs with MCTs, where ECT and IL-12 GET did not lead to major shifts. We were unable to establish any association between the expression of immune markers and the microbiota. Full article

Type II collagen (CII), the major structural protein in the cartilage extracellular matrix, is a promising biomaterial for scaffold design in cartilage tissue engineering. In this study, high-purity CII was successfully extracted from bovine cartilage, an abundant by-product of cattle slaughter, and its amino acid composition, triple-helical conformation, and thermal stability were verified. CII was subsequently combined with silk fibroin (SF) and chitosan (CS) to fabricate three-dimensional (3D) porous scaffolds via freeze-drying. The pore structure, porosity, swelling behavior, mechanical properties and in vitro degradation characteristics were systematically evaluated. Scaffolds with favorable structural integrity, mechanical performance, and degradation rates were further evaluated biologically using human primary chondrocytes. All CII-based composite scaffolds supported chondrocyte growth and promoted early extracellular matrix deposition. Notably, the scaffold with a CII:SF:CS ratio of 7:3:1 showed the highest GAG/DNA content, accompanied by upregulated gene expression related to the cartilage phenotype (COL2A1, ACAN, and SOX9) and reduced expression of the dedifferentiation marker COL1A1, indicating improved phenotype maintenance. Overall, within the tested range, CII70 (CII:SF:CS = 7:3:1) represents a practical compromise between scaffold stability and in vitro chondrocyte-related outcomes, providing a basis for selecting CII/SF/CS formulations for cartilage tissue engineering. Full article

Soil ciliates are an important component of the soil micro-food web, playing key roles in organic matter decomposition and nutrient cycling. However, research on the species diversity and taxonomy of this group in the temperate forest soils of China is still limited. This study investigates the morphology and ciliary pattern of two ciliate species discovered in the Changbai Mountain region of northeastern China: Bryometopus changbaishanensis sp. n. and Apocolpodidium etoschense Foissner et al., 2002, using live observation and silver carbonate impregnation. B. changbaishanensis sp. n. is characterized by the following morphological features: size in vivo approximately 40–48 × 20–29 μm, 11–14 somatic kineties; the paroral membrane consists of about 16–26 dikinetids; and there are 11–15 oral membranelles. This species differs from B. atypicus in its smaller body size in vivo, fewer somatic kineties, and fewer oral membranelles. Apocolpodidium etoschense Foissner et al., 2002, exhibits the following morphological features: in vivo size approximately 48–85 × 19–35 μm, 16–20 somatic kineties, and a gently curved paroral membrane composed of about 13–20 dikinetids; its hypostomial organelle consists of three to five files, each containing approximately three to five monokinetids. Additionally, DNA extraction and SSU rRNA gene sequencing were performed to elucidate their evolutionary relationships. Phylogenetic analyses based on SSU rRNA gene data indicated that Bryometopus changbaishanensis sp. n. clusters with B. atypicus. This study also provides a redescription and supplementary definition of A. etoschense, with the Changbai Mountain population forming a fully supported cluster with previously sequenced data. Full article

This study focused on optimizing endoglucanase production using a peculiar fungal co-culture comprising Rhizopus arrhizus and Aspergillus fumigatus, identified through morphological and 18S rDNA analyses. The co-culture achieved the highest enzyme production after 72 h of fermentation with alkaline-treated substrates. Scanning Electron Microscopy (SEM) revealed substantial structural disruption in pretreated biomass, enhancing enzyme accessibility. Among the tested substrates, pea hulls proved to be the most effective for enzyme production. Optimization of physical and nutritional parameters was performed using Design of Experiments (DOE) approaches, specifically Plackett–Burman Design (PBD) for screening and Central Composite Design (CCD) for fine optimization. The maximum endoglucanase activity of 119.58 U/mL/min was obtained under the optimized conditions of 27.5 °C, pH 5.5, inoculum age 3.5 days, and supplementation with 1.5% fructose, 1.25% yeast extract, 1.25% sodium nitrate, and 1.25% Tween 80. Analysis of Variance (ANOVA) confirmed the significance of these parameters and their interactions at a 95% confidence level, with a strong model fit (R² = 0.9052). This study demonstrates the potential of waste pea hulls as a cost-effective substrate for enzyme production, supporting waste valorization and contributing to a circular bioeconomy through sustainable biomass utilization. Full article

Hospital environments host diverse microbial communities that may contribute to nosocomial infections. Moisture-retaining surfaces such as cleaning sponges and faucet edges represent high-contact, under-investigated hygiene hotspots, particularly in wards caring for immunocompromised patients. Environmental samples were collected from cleaning sponges (n = 14) and faucet edges (n = 4) across multiple hospital rooms of a paediatric haematology–oncology unit, with domestic physician sponges as controls (n = 3). DNA was extracted and sequenced targeting the V3–V4 and V7–V9 hypervariable regions of the 16S rRNA gene on the Illumina MiSeq platform. Taxonomic composition and alpha/beta diversity were assessed using QIIME 2 and R. Sponge samples were dominated by Moraxellaceae, particularly Acinetobacter and Enhydrobacter, and showed significantly lower alpha diversity than faucet samples (Shannon index: Kruskal–Wallis H = 8.4, p = 0.01; Faith’s phylogenetic diversity: H = 9.17, p = 0.01). Faucet samples were enriched in human-associated genera including Staphylococcus, Streptococcus, and Chryseobacterium. Statistically significant beta-diversity differences were detected between sponge and faucet communities by PERMANOVA based on Bray–Curtis dissimilarity (p = 0.01), whereas no significant clustering by room or floor location was observed (p = 0.29). Potentially pathogenic taxa including Aeromonas, Pseudomonas, and Enterobacteriaceae were identified across both surface types. Domestic control sponges showed distinct microbiome profiles from hospital samples. Microbial communities differ significantly between hospital sponges and faucets, with surface type rather than location as the primary determinant of community structure. The presence of opportunistic pathogens on both surface types highlights the importance of enhanced hygiene protocols, inclusion of faucet edges and sink drains in routine decontamination schedules, and regular microbiological surveillance in clinical settings caring for immunocompromised patients. Full article

Background/Objectives: Liquid profiling of molecular and epigenetic markers in bodily fluids is an expanding field of cancer biomarker research. Recent research activity also reveals the human satellite 2 (HSAT2) repetitive element cell-free DNA (cfDNA) as a potential cancer biomarker. Based on our recent results from targeted sequencing of HSAT2 cfDNA, we tested whether a specific HSAT2 sequence (e.g., 95 bp-HSAT2) shows greater cancer enrichment than 114 bp-SAT2, from which it derives, in patients with colon cancer. Methods: By comparing the ratio of 114 bp-HSAT2 to 95 bp-HSAT2, we investigated the increased cancer enrichment of 95 bp-HSAT2 in cfDNA samples obtained from plasma DNA extraction and a hybridization capture assay, in which HSAT2 sequences were captured from plasma using a biotin-labeled probe, in samples from colon cancer patients (n = 60) and polyp-controls (n = 60), and polyp-free controls (n = 60). Results: A correlation analysis between Ct values from DNA extraction and the hybridization capture assay for both 95 bp- and 114 bp-HSAT2 showed a positive correlation in patients with colon cancer and control subjects, indicating that the hybridization capture assay provides HSAT2 levels comparable to those obtained by DNA extraction. With both approaches, we found a lower 114 bp-HSAT2 to 95 bp-HSAT2 ratio in patients with colon cancer than in the control groups. The median ratio of extracted DNA was 62, 78, and 79 in patients with colon cancer, polyp-controls (p = 0.23), and polyp-free controls (p = 0.067), respectively. Capture assay values were 49, 87, and 64 in patients with colon cancer, polyp controls (p = 0.016), and polyp-free controls (p = 0.19), respectively. Even though statistical significance was not achieved in some comparisons, these results suggest that 95 bp-HSAT2 is more abundant in the blood of patients with colon cancer than 114 bp-HSAT2 in non-malignant patients. Conclusions: To our knowledge, this is the first study to conduct a hybridization capture assay using a biotinylated probe as a feasible approach for targeted enrichment of cfDNA from plasma. Our results confirm the outcomes of our recent article based on targeted sequencing and reveal that some specific HSAT2 sequences may exhibit increased cancer abundance. Full article

The fruits of Solanum lycopersicum L. cultivar “Microtom” are a powerful source of antioxidants. We investigated whether two light-quality regimes, i.e., fluorescent white (FL) and red-blue (RB), influenced the antioxidant composition in such fruits, and assessed the potential radioprotective properties of their extracts on normal human cells exposed to clinical photons as used in cancer radiotherapy (RT). Increasing normal-tissue tolerance to radiation is critical for reducing the risk of RT-associated sequelae. Biochemical characterization showed that RB enhanced the content of antioxidant phytochemicals (i.e., polyphenols, flavonoids, total carotenoids, lycopene), while FL promoted ascorbic acid synthesis. Initially tested at 200 µg/mL, RB-derived extracts decreased radiation-induced DNA damage as measured by the cytokinesis-block micronucleus (CBMN) assay in epidermal HaCaT cells. Both RB and FL regimes were subsequently studied in MCF-10A breast cancer (BC) cells, a model of normal-tissue radioresponse in BC RT, using extracts at 100 and 200 µg/mL and also evaluating oxidative stress by a ROS detection assay. Both FL and RB afforded radioprotection. However, RB suppressed radiation-induced MN formation and oxidative stress to a greater extent compared to FL. Therefore, modulation of light-quality regimes represents an innovative approach for developing radionutraceuticals with potential benefits for RT patients. Full article

Background: The individual and social burden of endometriosis is high, and the diagnosis is usually delayed by 7–10 years. Menstrual effluent (ME) represents an accessible and uniquely informative biofluid. This systematic review evaluated the pathophysiological relevance and diagnostic potential of ME in endometriosis. Methods: Following PRISMA 2020 guidelines, we systematically searched PubMed/MEDLINE, EBSCOhost (Academic Search Premier, APA PsycArticles, APA PsycInfo, CINAHL, and MEDLINE), Semantic Scholar, and Google Scholar from inception to 30 November 2025. Original studies analyzing human ME or ME-derived cells in women with endometriosis versus controls were eligible. We extracted study design, analytic methods, diagnostic accuracy metrics (AUC, sensitivity, and specificity), mechanistic pathways, and risk of bias (QUADAS-2 for diagnostic, and NIH tools for mechanistic studies). Results: Thirty-five studies were included. ME consistently captured key pathophysiological mechanisms of endometriosis, including impaired decidualization and progesterone resistance, immune dysregulation with diminished cytotoxic clearance, pro-angiogenic and invasive phenotypes, heightened stem/progenitor cell survival, cellular senescence and DNA damage, and altered extracellular-vesicle signaling. Diagnostic accuracy was reported in nine studies. Aromatase mRNA showed the highest performance (AUC 0.977), followed by TGF-β1 (AUC 0.973) and IGFBP1 (AUC 0.92). A lipidomic two-marker model achieved an AUC of 0.87. All diagnostic assessments were based on case–control studies; none conducted prospective validation. Conclusions: ME is a biologically relevant, non-invasive, and patient-acceptable biospecimen reflecting core endometriosis mechanisms and yielding promising diagnostic accuracy. The highest diagnostic performance was achieved for assays reflecting steroidogenic and growth-factor pathways (e.g., aromatase and TGF-β1). Standardization and prospective validation are needed before clinical adoption. Full article

In order to establish a rapid and sensitive LAMP visual detection method for Cherry Virus A on-site, this study used the conserved fragment of the CVA coat protein (CP) sequence as a template for primer design. The rapid visual LAMP detection method for Cherry Virus A was successfully established by optimizing the reaction system components (concentration ratio of internal and external primers, and concentrations of loop primers, Bst DNA, Mg²⁺, dNTPs and betaine) and reaction conditions (temperature and time). This method enables specific detection of Cherry Virus A and facilitates visual inspection of crude nucleic acid extracts within 40 min, significantly reducing the diagnostic turnaround time. The limit of detection is 67.54 pg μL⁻¹ (cDNA), which is 100 times more sensitive than PCR. Analysis of 70 field sweet cherry samples revealed an RT-LAMP positivity rate of 91.42%, significantly surpassing the 71.42% achieved by RT-PCR. This method is suitable for the rapid on-site detection of Cherry Virus, and can also provide a theoretical reference for the early diagnosis of cherry viral diseases. Full article

Background: Obesity is a multifactorial chronic disease resulting from sustained energy imbalance and modulated by environmental and demographic factors, and it is associated with numerous comorbidities. DNA methylation is an epigenetic modification associated with obesity. Modulation of DNA methylation is a viable target for obesity control strategies. The flavanol (-)-epicatechin (EC) exerts beneficial effects in overweight individuals, suggesting that EC may influence gene regulation through signaling pathways and epigenetic mechanisms. We evaluated whether EC modulates obesity-associated DNA methylation changes using complementary in silico, in vitro, and in vivo approaches. Methods. In silico analyses were performed to explore potential EC interactions with the DNA methyltransferases DNMT1, DNMT3A, and DNMT3B. DNMT activity was measured in nuclear extracts of 4T1 cells in the presence of EC. Finally, in a C57BL/6 mouse model of diet- induced obesity, we assessed global DNA methylation and the expression of the DNA methyltransferases, as well as metabolism-related genes; peroxisome proliferator-activated receptor gamma coactivator 1 alpha (Pgc-1α), pyruvate dehydrogenase kinase isozyme 4 (Pdk4), and nuclear factor erythroid 2–related factor 2 (Nrf2) and relative mitochondrial DNA content (mtDNA/nDNA ratio) in visceral adipose tissue (VAT) and skeletal muscle. Results. EC showed stable in silico interactions within catalytic/cofactor-binding regions of DNMTs and inhibited DNMT activity in vitro in a concentration-dependent manner. In vivo, the obesogenic diet reduced global DNA methylation and decreased transcript levels of Dnmt1, Dnmt3a, and Dnmt3b in skeletal muscle and adipose tissue. EC counteracted obesity-associated DNA methylation changes in skeletal muscle, restoring global methylation and Dnmt expression toward control levels, whereas effects in VAT were limited. EC increased mitochondrial DNA content. Discussion. In silico and enzymatic data suggest that EC may bind DNMT active sites and inhibit DNMT activity in a concentration-dependent manner, supporting a role for EC in obesity-related epigenetic remodeling, particularly in skeletal muscle. EC also increased relative mitochondrial DNA content in VAT and skeletal muscle despite no obesogenic diet effect on relative mitochondrial abundance, consistent with favorable mitochondrial modulation. In conclusion, EC is an epigenetic modulator and may have positive effects in obesity related dysfunctional tissues. Full article

Brazilian microalgae represent an underexplored reservoir of bioactive compounds with promising biotechnological and dermocosmetic applications. In this study, eight native Brazilian microalgae strains were cultivated under control (C) and stress conditions, nitrogen depletion (N) and salt stress (S), to modulate their bioactive profiles. Derived acetone extracts (24 samples) were evaluated for their antioxidant and antibacterial activities relevant to skin health. The antioxidant capacity of extracts was assessed by three complementary methods: ferric reducing antioxidant power (FRAP), 2,2-diphenyl-1-picryl-hydrazyl (DPPH) and superoxide anion radicals scavenging. Additionally, the antibacterial effects against four skin microorganisms (Staphylococcus epidermidis, Staphylococcus hominis, Staphylococcus aureus, and Cutibacterium acnes) were also assessed. Among the tested samples, extracts from Scenedesmus armatus (Extract 40C) and from Chlorella sorokiniana (Extract 198C) displayed the highest antioxidant potential, with DPPH radical reduction of 22.6 ± 1.6% and 20.7 ± 1.9% and FRAP values of 178.3 and 156.8 μmol FeSO₄/g extract, respectively. Superoxide scavenging assays showed IC₅₀ values of 150.9 μg/mL for sample 40C and 139.6 μg/mL for sample 198C. Regarding the antibacterial assay, the IC₅₀ values for S. epidermidis were notable, with sample 198C exhibiting the highest potency (10.3 µg/mL), closely matching the standard drug (12.4 µg/mL). The inhibitory capacity against C. acnes showed that samples 40C (58.4 µg/mL) and 198C (83.5 µg/mL) demonstrated antimicrobial relevance. Mechanistic assays suggested that the antibacterial effects of both samples may involve alterations in bacterial membrane integrity and DNA damage. Overall, these findings highlight the dermocosmetic potential of native Brazilian microalgae, still largely untapped in biotechnology, as natural sources of multifunctional ingredients for the development of sustainable skin care formulations. Full article

TP53 is a tumor-suppressor gene involved in regulating apoptosis, DNA repair, and genomic stability. Mutations in TP53 are implicated in approximately half of all detected cancers, including breast, lung, colorectal, and ovarian cancers, making it a significant target for therapeutic interventions. Many pharmaceutical drugs aim to restore TP53 function, and there is a need for predictive tools to assess how compounds may affect TP53 expression. In this study, we propose a new ensemble machine-learning model to predict the direction of TP53 relative gene expression in response to pharmaceutical compounds. Our model utilizes molecular fingerprints, descriptors, and scaffold-based features extracted from SMILES representations of compounds concatenated into a single feature vector. Trained using our newly generated benchmark dataset based on the Connectivity Map (CMap) database and addressing class imbalance with the Synthetic Minority Over-sampling Technique (SMOTE), our model achieves 62.9%, 93.9%, 40.3%, and 0.39 in terms of accuracy, sensitivity, specificity, and Matthews Correlation Coefficient (MCC), respectively. As the first-of-its-kind TP53 gene regulation prediction, our study serves as a convincing proof-of-concept that paves the way for future investigation. GenReP as a stand-alone predictor, its source code, and our newly generated benchmark dataset are publicly available. Full article