Search Results (4,211)

Mining novel Streptomyces species from extreme environments provides a valuable strategy for the discovery of new antibiotics. Here, we report a strain of Streptomyces sp. HMX87^T, which exhibits antimicrobial activity and was isolated from desert soil collected in the Tuha Basin, China. Molecular taxonomic analysis revealed that the 16S rRNA gene sequence of strain HMX87^T shares the highest similarity with those of Streptomyces bellus CGMCC 4.1376^T (98.5%) and Streptomyces coerulescens DSM 40146^T (98.43%). In phylogenetic trees, it formed a distinct branch. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain HMX87^T and the above two type strains were below the thresholds of 95% and 70%, respectively, confirming that strain HMX87^T represents a novel species within the genus Streptomyces, for which the name Streptomyces hamibioticus sp. nov. is proposed. Physiologically, the strain HMX87^T grew at temperatures ranging from 25 to 37 °C, tolerated pH values from 5 to 12, and survived in NaCl concentrations of 0% to 8% (w/v). Chemotaxonomic characterization indicated the presence of LL-diaminopimelic acid (LL-DAP) in the cell wall, ribose and galactose as whole-cell hydrolysate sugars, MK-9(H8) (66.3%) as the predominant menaquinone, and iso-C_16:0 (25.94%) and anteiso-C_15:0 (16.98%) as the major fatty acids characteristics that clearly distinguish it from its closest relatives. Whole-genome sequencing of strain HMX87^T revealed an abundance of genes associated with high-temperature tolerance, salt-alkali resistance, and antimicrobial activity. The genomic features and secondary metabolic potential reflect its adaptation to extreme environmental conditions, including high temperature, salinity, alkalinity, strong ultraviolet radiation, and oligotrophic nutrients. The strain HMX87^T has been deposited in the Czech Collection of Microorganisms (CCM 9454^T) and the Guangdong Microbial Culture Collection Center (GDMCC 4.391^T). The 16S rRNA gene and whole-genome sequences have been submitted to GenBank under accession numbers PQ182592 and PRJNA1206124, respectively. Full article

Mesenchymal stem cells (MSCs) spontaneously assemble into three-dimensional (3D) spheroids under matrix-deficient conditions such as the synovial cavity, although their functional significance has yet to be fully elucidated. In this study, we used concave microwell cultures to promote the spontaneous aggregation of adipose-derived MSCs (ASCs) from OA patients, thereby mimicking the intra-articular microenvironment. We analyzed the paracrine factors of ASC aggregates and compared it with that of conventional 2D monolayer cultures. Notably, 3D aggregation significantly increased the secretion of HGF and VEGF, whereas FGF2 levels remained relatively unchanged. These results indicate that the structural characteristics of ASC aggregates enhance the secretion of key paracrine factors involved in angiogenesis and tissue repair. To functionally evaluate the biological relevance of the secreted factors, conditioned media (CM) from ASC aggregates were applied to human articular chondrocytes. The CM significantly promoted chondrocyte proliferation, an effect that was abolished by the addition of HGF-neutralizing antibodies, thereby highlighting HGF as a central mediator of the regenerative response. Additionally, we further explored whether extracellular factors could modulate growth factor expression such as HGF. In this context, we investigated the impact of low-concentration hyaluronic acid (HA), a key synovial component widely used in OA treatment. Co-treatment with HA not only amplified the expression and secretion of HGF, VEGF, and FGF2, but also promoted ASC proliferation. ASCs forming functional aggregates may exert regenerative effects as active paracrine modulators, and the addition of low-dose hyaluronic acid is expected to further enhance this function, offering a promising strategy for MSC-based osteoarthritis therapy. Full article

Objectives: Lepidium meyenii Walpers (LMW), a high-altitude plant, is known to stimulate hormone release, counteract neurodegeneration, and protect against oxidative stress. Saliva is vital for oral health, and reduced production leads to xerostomia, often caused by aging, radiation, or Sjögren’s syndrome. Key pathological features include mesenchymal fibrosis and acinar atrophy, largely regulated by the TGF-β1 pathway. Current treatments are limited, with many patients relying on artificial saliva. Developing therapies to restore salivary function could offer significant benefits. Methods: In this study, we assessed the protective effects of LMW extract (LMWE) in irradiated C57BL/6J mice and TGF-β1-treated rat parotid acinar cells (Par-C10) using histological, molecular, bioenergetic, and 3D organoid analyses to evaluate salivary gland regeneration and lineage-specific differentiation. Results: LMWE significantly restored gland weight, shortened secretion lag time, and increased amylase activity in irradiated mice. Histological and molecular analyses showed reduced acinar atrophy and fibrosis, preservation of epithelial polarity, and upregulation of Mist1, AQP5, and amylase. In vitro, LMWE protected Par-C10 cells from TGF-β1-induced senescence, preserved mitochondrial membrane potential, and improved epithelial barrier function. In 3D organoid cultures of Par-C10 cells embedded in matrix, (1E,4Z)-1-(2,4-dihydroxyphenyl)-5-(3,4-dihydroxyphenyl) penta-1,4-dien-3-one (DHPPD) and (Z)-N-phenyldodec-2-enamide (E4Z-PD)-selectively enhanced acinar and ductal lineage differentiation, respectively. Conclusions: These results suggest that LMWE promotes salivary gland regeneration through antioxidative and lineage-specific mechanisms and may represent a safe and effective therapeutic strategy for xerostomia. Full article

The growing threat of Antimicrobial Resistance (AMR) demands innovative drug discovery, yet conventional 2D cell cultures fail to accurately mimic in vivo conditions, leading to high failure rates in preclinical studies. This review addresses the critical need for more physiologically relevant platforms by exploring recent advancements in bioengineered 3D tissue models for studying bacterial pathogenesis and antimicrobial drug discovery. We conducted a systematic search of peer-reviewed articles from 2015 to 2025 across PubMed, Scopus, and Web of Science, focusing on studies that used 3D models to investigate host–pathogen interactions or antimicrobial screening. Data on model types, biomaterials, fabrication techniques, and key findings were systematically charted to provide a comprehensive overview. Our findings reveal that a diverse range of biomaterials, including biopolymers and synthetic polymers, combined with advanced techniques like 3D bioprinting, are effectively used to create sophisticated tissue scaffolds. While these 3D models demonstrate clear superiority in mimicking biofilm properties and complex host–pathogen dynamics, our analysis identified a significant research gap: very few studies directly integrate these advanced bioengineered 3D models for high-throughput antimicrobial drug discovery. In conclusion, this review highlights the urgent need to bridge this disparity through increased research, standardization, and scalability in this critical interdisciplinary field, with the ultimate goal of accelerating the development of new therapeutics to combat AMR. Full article

In our previous study, adipose-derived stem cells (ASCs) cultured in a three-dimensional (3D) organotypic system exhibited mesenchymal-to-epithelial transition (MET) features, including cobblestone morphology and increased expression of E-cadherin and CK18. In this study, we investigated whether ionizing radiation could reverse this phenotype via epithelial–mesenchymal transition (EMT) and examined the involvement of Notch signaling. Mouse ASCs were cultured in Matrigel-based 3D organotypic conditions and exposed to 8 Gy of γ-radiation, and EMT- and Notch-related gene and protein expression were assessed 96 h post-irradiation using ATP viability assays, RT-qPCR, and Western blotting. Exposure to 8 Gy significantly reduced cell viability in 2D ASCs to 49.50 ± 6.50% compared with 61.02 ± 5.77% in 3D organoids (p < 0.0001). Irradiated 3D organoids showed EMT-like changes, including an increase of ~2.5-fold in fibronectin and an increase of ~2.0-fold in Twist1 expression, while epithelial CK18 was modestly elevated. Notch signaling was concurrently activated, with Notch1 and Jagged1 increasing by more than twofold and Fra-1 being significantly upregulated. Pretreatment with 20 μM of the γ-secretase inhibitor (GSI) kept cell viability above 90% and suppressed radiation-induced fibronectin, Twist1, Notch1, and Jagged1 expression. These findings indicate that ionizing radiation promotes EMT in 3D-cultured ASCs and reverses prior epithelialization, with Notch signaling playing a key regulatory role. The 3D ASC organoid model may thus provide a physiologically relevant platform for investigating radiation-induced plasticity and potential antifibrotic interventions. Full article

Background/Objectives: Mesenchymal stem cells (MSCs) offer promising prospects for novel treatment modalities in cellular therapies and artificial organ production. Despite a surge in artificial tissue research, there is a dearth of comprehensive studies detailing the entire process from stem cells to tissue production, coupled with a scarcity. This study, however, presents the utility of extra-embryonic MSCs derived from placental tissue, traditionally considered as medical waste. Methods: Within a 3-dimensional cell culture system, histological assessments, and comprehensive optimization studies, the entire process required for artificial tissue production is addressed. Results: The results obtained are encouraging regarding the advancement of cellular therapies and artificial tissue engineering. However, challenges such as biopolymer degradation highlight the necessity for multistep approaches. Each analysis within this study delves into the discussion and optimization of key steps in artificial tissue production. Conclusions: Consequently, this study not only represents one of the first of its kind but also lays the groundwork for future investigations into relevant clinical applications. Full article

Metabolic engineering of mesenchymal stem/stromal cells (MSCs) represents a compelling frontier for advanced cellular therapies, enabling the precise tuning of their biological outputs. This feature paper examines the critical role of engineered culture microenvironments, specifically 3D platforms, hypoxic preconditioning, and other priming approaches, which are synthetic biology strategies used to guide and optimize MSC metabolic states for desired functional outcomes. We show that these non-genetic approaches can significantly enhance MSC survival, immunomodulatory capacity, and regenerative potential by shifting their metabolism toward a more glycolytic phenotype. Furthermore, we propose a new paradigm of “designer” MSCs, which are programmed with synthetic circuits to sense and respond to the physiological cues of an injured microenvironment. This approach promises to transform regenerative medicine from an inconsistent field into a precise, predictable, and highly effective therapeutic discipline. Full article

Multipotent hematopoietic stem cells (HSC) reside in specialized niches of the bone marrow (BM). The maintenance of their stemness requires a precisely regulated bone marrow microenvironment (BMM), supported by mesenchymal stem cells (MSCs), stromal reticular cells, and endothelial and nerve cells located within the vascular and endosteal niches. The heterogeneity of the niche environment is caused by the diversity of cell populations from HSCs to more mature hematopoietic cell types and MSCs, which collectively influence the complex intercellular interactions involved in hematopoiesis. MSC subclusters in BM are characterized by the phenotypes of CXC-chemokine ligand 12, leptin receptor, neuron-glial antigen 2, and Nestin+ cells. The article presents a detailed characterization of individual stem cell types in the BM, their reciprocal interaction, and the possibility of in vitro simulation of the bone marrow niche as a dynamic structure. Development of a suitable simulation of the BMM is essential for advancing research into both physiological and pathological processes of hematopoiesis. The main goal is to simulate 3D cell culture using biomaterials that mimic the BM niche in the form of hydrogels and scaffolds, in combination with extracellular matrix components. Full article

Plant cell cultures offer a promising platform for producing valuable biomolecules, yet their use in bioreactors remains under-optimized. Compared to animal or microbial cells, plant cells grow more slowly, limiting productivity. A common bioprocess strategy to improve yields involves controlling dissolved oxygen (DO) levels. However, little research has focused on combining agitation and aeration to regulate oxygen in plant cell cultures within bioreactors. The aim of this study was to evaluate the impact of an oxygen cascade mixing agitation and aeration on plant cell growth in stirred-tank systems. By maintaining 30% DO through this approach, the specific growth rate (µ) increased from 0.082 d⁻¹ to 0.144 d⁻¹ on average in Nicotiana benthamiana cultures at the 2 L scale, decreasing batch lengths from 21 to 10 days. These conditions were successfully replicated in a 7 L stainless-steel pilot bioreactor using previous values of geometry, k_La and N_RE as scale-up criteria, obtaining a µ of 0.161 d⁻¹. These results demonstrate that plant cell cultures’ efficiency can be enhanced by using standard bioprocess parameters. While this work confirms the feasibility of cascade oxygen control for improvements in growth, further studies are needed to evaluate its specific impact on biomolecule production across different systems. Full article

Organoids, self-organizing, three-dimensional (3D) multicellular structures derived from tissues or stem cells, offer physiologically relevant models for studying human development and disease. Compared to conventional two-dimensional (2D) cell cultures and animal models, organoids more accurately recapitulate the architecture and function of human organs. Among the critical microenvironmental cues influencing organoid behavior, hypoxia and multilineage communication are particularly important for guiding cell fate, tissue organization, and pathological modeling. Hypoxia, primarily regulated by hypoxia-inducible factors (HIFs), modulates cellular proliferation, differentiation, metabolism, and gene expression, making it a key component in disease modeling. Similarly, multilineage communication, facilitated by intercellular interactions and extracellular matrix (ECM) remodeling, enhances organoid complexity and immunological relevance. This review explores the dynamic interplay between hypoxia and multilineage signaling in 3D organoid-based disease models, emphasizing recent advances in engineering hypoxic niches and co-culture systems to improve preclinical research fidelity. We also discuss their translational implications for drug screening, regenerative medicine, and precision therapies, while highlighting current challenges and future opportunities. By integrating biophysical, biochemical, and computational approaches, next-generation organoid models may be further optimized for translational research and therapeutic innovation. Full article

The search for markers applicable for efficient differential diagnosis and personalized therapy is a priority task of experimental neuro-oncology. Modern molecular methods allow us to analyze human biopsy material; however, further actions with this extracted tumor tissue are limited. Relevant and sophisticated CNS tumor models are required for precise therapy development. Although it is possible to use human biomaterial to create 2D and 3D cultures and implant them into xenograft animals, the data generated from such models is limited. Due to changes in the classification of the CNS tumors in 2021, a representative model should have not only morphological similarity to human tumors but also key genetic aberrations for studying the mechanisms of carcinogenesis and personalized therapy (such as PDGFRa, Olig1/2, Sox2, and Mki67) for different glioma models such as astrocytoma, oligodendroglioma, and glioblastoma. On the basis of a unique scientific facility “The Collection of experimental tumors of the nervous system and neural tumor cell lines” (Avtsyn Research Institute of Human Morphology of “Petrovsky National Research Center of Surgery”), there is a biobank of chemically induced transplantable tumors of laboratory animals. Their properties, mechanisms, and progression closely correlate with malignant CNS neoplasms in humans. These are potentially useful for identifying novel signaling pathways associated with oncogenesis in the nervous system and personalizing therapeutic approaches. In our work, we characterized a tissue-transplantable brain tumor strain of rat glioma101.8 using MRI, IHC, scRNA-seq, and qPCR-RT methods. According to this study, the cellular composition of the tissue-transplantable rat glioma 101.8 strain was determined, as well as the major genetic signature characteristics of each cell population of this tissue-transplantable strain and its microenvironment. Full article

Microphysiological systems (MPSs), such as organ-on-a-chip platforms, are promising alternatives to animal testing for drug development and physiological research. The BioStellar™ Plate is a commercial MPS platform featuring an open-top culture chamber design with on-chip stirrer pumps that circulate culture medium through six independent, dual microchannel-connected chamber multiorgan units. Although this design enables a circular flow, the open-top culture chamber format prevents the application of fluidic shear stress, a force that cells experience in vivo, which affects their behavior and function. To address this, we developed two fluidic shear stress attachments for the BioStellar™ Plate. These attachment channel fluids provide controlled mechanical stimulation to cultured cells. The flow dynamics were simulated using COMSOL Multiphysics to estimate shear stress levels. The attachments were fabricated and validated through fluorescent bead tracking and biological assays. The FSSA-D is designed for flat-bottom standard cell cultures, while the FSSA-I is designed for epithelial monolayers, enabling the application of fluidic shear stress across the basal membrane. Experiments with intestinal epithelial cells (Caco-2) demonstrated that both attachments enhanced cell barrier function under a fluidic environment, as indicated by higher transepithelial electrical resistance (TEER). These findings demonstrate that the attachments are practical tools for mechanobiology research with MPS platforms. Full article

Articular cartilage regeneration remains a major challenge due to its limited self-repair capacity. Bone marrow-derived skeletal stem cells (SSCs) and mesenchymal stem cells (MSCs) are promising candidates for cartilage engineering, although they differ in their chondrogenic potential. This study explored whether co-culturing SSCs and MSCs in three-dimensional (3D) organoid systems under cartilage physioxia (5% O₂) and chondrogenic induction could improve cartilage tissue formation. SSCs, MSCs, and SSC–MSC co-cultures were characterized for morphology, phenotype, and differentiation capacity. Organoids were generated and cultured for 10 days, followed by analysis of morphology, viability, gene expression (SOX9, RUNX2, ACAN, COL2A1, COL10A1, PRG4, and PDPN), chondrocyte-associated antigens (CD44, CD105, CD146, and PDPN), and cartilage ECM proteins (aggrecan, collagen types I, II, and X, and PRG4). SSCs showed robust chondrogenic and osteogenic potential, while MSCs exhibited a balanced multipotency. Co-culture-derived organoids enhanced chondrogenesis and reduced adipogenesis, with higher expression of cartilage-specific ECM and lower hypertrophic marker levels. These findings highlight the functional synergy between SSCs and MSCs in co-culture, promoting the formation of stable, cartilage-like structures under physioxia. The approach offers a promising strategy for generating preclinical models and advancing regenerative therapies for hyaline cartilage repair. Full article

Aims: Surgery remains the only definitive treatment option for abdominal aortic aneurysms (AAA), as no conclusive evidence supports drug effectiveness in preventing AAA growth. Although type 2 diabetes (T2D) is an important cardiovascular risk factor, patients with T2D show reduced AAA presence and growth, associated with metformin use. We aimed to investigate the potential benefits of metformin on AAA using proteomics and in vitro experiments. Methods: Proteomics analysis using tandem mass spectrometry was performed on aortic smooth muscle cells (SMCs) from non-pathological controls (C-SMC, n = 8), non-diabetic (ND, n = 19) and diabetic (D, n = 5) AAA patients. Key findings were subsequently validated in aortic tissue using mass spectrometry-based proteomics. SMCs were cultured with/without metformin and analyzed. Results: Comparison of the proteome of SMCs from ND-AAA patients with controls revealed a reduction in proteins associated with metabolic processes and mitochondrial function. Cytoskeletal and extracellular matrix (ECM) proteins were elevated in ND-AAA-SMCs versus C-SMCs, with a similar cluster of mechanosensitive proteins being increased in ND-AAA-SMCs versus D-AAA-SMCs. D-AAA-SMCs showed an improved metabolic and antioxidant profile, enriched in pentose phosphate pathway proteins responsible for NAD(P)H generation (G6PD, PGD) and NAD(P)H-dependent antioxidants (NQO1, CBR1, AKR1C1, AKR1B1, GSTM1), all regulated by NRF2, an antioxidant transcription factor. Over half of the proteins identified in the protein–protein interaction network, constructed from proteins with higher expression in D-AAA SMCs versus ND-AAA SMCs, were verified in D-AAA aortic tissue. In vitro, metformin causes a shift from aerobic to anaerobic metabolism, increased AMPK activation and elevated mitochondrial biogenesis, indicated by increased PGC-1α expression. Metformin increased the gene expression of PGD, CBR1 and the protein expression of NQO1, with enhanced translocation of pNRF2 to the nucleus, due to reduced KEAP1 as negative regulator of NRF2. Consequently, metformin enhanced the gene expression of well-known antioxidant regulators SOD2 and CAT. Conclusions: This study identified significant differences in the proteome of SMCs derived from controls, ND-AAA and D-AAA patients. It highlights distinct pathways in relation to mechanosensing, metabolism and redox balance as therapeutic targets of metformin that may underlie its inhibition of AAA progression. Full article

Mesenchymal stromal/stem cells (MSCs) are known to secrete a wide range of pleiotropic molecules promoting tissue repair and regeneration. Recent advances in cell sheet technology have demonstrated significant improvements in the regenerative capacity of MSCs within the sheet, retaining appropriate microenvironmental cues, and have suggested an instructing role of extracellular matrix (ECM). We previously found that the secretome of MSCs cultured on a decellularized MSC-derived ECM (dECM) was significantly enriched in dozens of cytokines, chemokines and growth factors compared to the secretome of MSCs grown on standard plastic dishes. The enriched secretome has been shown to have enhanced chemotactic and angiogenic properties, stimulate C2C12 myoblast proliferation and promote skeletal muscle regeneration in a murine in vivo model. Here, we report novel findings about dECM-induced changes in the miRNA profile of MSCs. We performed miRNA-seq and found 17 differentially expressed miRNAs in endometrial MSCs (MESCs) with miR-146a-5p being the most upregulated. Additionally, we investigated miR-146a-5p expression in MSCs of various origins after exposure to dECM, and found a correlation between miR-146a-5p upregulation and the general dECM-induced paracrine response. Furthermore, we demonstrated that miR-146a-5p mimics, transfected into C2C12 myoblasts, promoted their proliferation, suggesting a role for miR-146a-5p in myotropic effects mediated by the enriched secretome. These findings provide new insights into how ECM as a component of the MSC niche influences the secretory phenotype and modulates therapeutic properties of MSCs. Full article