Silencing of microRNA-101 prevents IL-1β-induced extracellular matrix degradation in chondrocytes

Introduction: Extracellular matrix (ECM) degradation leads to malfunction of the cartilage in osteoarthritis (OA). Inflammatory cytokine interleukin-1 beta (IL-1 beta) functions in ECM degradation and prevents ECM synthesis by down-regulating the key transcription factor, Sox9, and consequently inhibiting ECM gene expression. Evidence reveals that microRNAs (miRNA) have been associated with OA, but little is known of their function in chondrocyte ECM degradation. This study aimed to identify possible miRNAs that mediate IL-1 beta-induced down-regulation of Sox9 as well as its known down-stream genes, collagen type II and aggrecan. Methods: The miRNAs were predicted based on three classical databases. The expression levels of the predicted miRNAs were assessed in IL-1 beta stimulated chondrocytes by real-time PCR. A luciferase reporter was used to test the binding of the miRNAs to the 3' untranslated regions (3'UTR) of Sox9. The predicted miRNAs were transfected into chondrocytes to validate their relationship with Sox9. Functional analysis of the miRNAs on chondrocytes ECM degradation was performed at both the mRNA and protein levels after miRNA transfection and IL-1 beta treatment. Results: Six miRNAs were predicted to target Sox9, and their expression in IL-1 beta-stimulated chondrocytes was revealed by real-time PCR. The luciferase reporter assay indicated that only miR-101 could bind to the 3' UTR of Sox9. The expression of Sox9 was likewise negatively regulated by miR-101 in rat chondrocytes. Functional analysis showed that miR-101 could aggravate chondrocyte ECM degradation, whereas miR-101 inhibition could reverse IL-1 beta-induced ECM degradation. Conclusion: miR-101 participates in IL-1 beta-induced chondrocyte ECM degradation. Down-regulating miR-101 expression can prevent the IL-1 beta-induced ECM degradation in chondrocytes. miR-101 probably functions by directly targeting Sox9 mRNA.http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000315192300044&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701RheumatologySCI(E)21ARTICLE6null1

m5U-SVM: identification of RNA 5-methyluridine modification sites based on multi-view features of physicochemical features and distributed representation

Abstract Background RNA 5-methyluridine (m5U) modifications are obtained by methylation at the C5 position of uridine catalyzed by pyrimidine methylation transferase, which is related to the development of human diseases. Accurate identification of m5U modification sites from RNA sequences can contribute to the understanding of their biological functions and the pathogenesis of related diseases. Compared to traditional experimental methods, computational methods developed based on machine learning with ease of use can identify modification sites from RNA sequences in an efficient and time-saving manner. Despite the good performance of these computational methods, there are some drawbacks and limitations. Results In this study, we have developed a novel predictor, m5U-SVM, based on multi-view features and machine learning algorithms to construct predictive models for identifying m5U modification sites from RNA sequences. In this method, we used four traditional physicochemical features and distributed representation features. The optimized multi-view features were obtained from the four fused traditional physicochemical features by using the two-step LightGBM and IFS methods, and then the distributed representation features were fused with the optimized physicochemical features to obtain the new multi-view features. The best performing classifier, support vector machine, was identified by screening different machine learning algorithms. Compared with the results, the performance of the proposed model is better than that of the existing state-of-the-art tool. Conclusions m5U-SVM provides an effective tool that successfully captures sequence-related attributes of modifications and can accurately predict m5U modification sites from RNA sequences. The identification of m5U modification sites helps to understand and delve into the related biological processes and functions

Biological Sequence Classification: A Review on Data and General Methods

With the rapid development of biotechnology, the number of biological sequences has grown exponentially. The continuous expansion of biological sequence data promotes the application of machine learning in biological sequences to construct predictive models for mining biological sequence information. There are many branches of biological sequence classification research. In this review, we mainly focus on the function and modification classification of biological sequences based on machine learning. Sequence-based prediction and analysis are the basic tasks to understand the biological functions of DNA, RNA, proteins, and peptides. However, there are hundreds of classification models developed for biological sequences, and the quite varied specific methods seem dizzying at first glance. Here, we aim to establish a long-term support website (http://lab.malab.cn/~acy/BioseqData/home.html), which provides readers with detailed information on the classification method and download links to relevant datasets. We briefly introduce the steps to build an effective model framework for biological sequence data. In addition, a brief introduction to single-cell sequencing data analysis methods and applications in biology is also included. Finally, we discuss the current challenges and future perspectives of biological sequence classification research

A first-principle study of the effect of Fe/Al impurity defects on the surface wettability of dolomite

The presence of Fe and Al atoms in large quantities in phosphate ores can significantly affect the surface properties of the minerals during flotation. In this study, the effects of Fe/Al impurities on the adsorption of H2O molecules on dolomite, including the density of states (DOS), Mulliken bond group values, and charge groups, were investigated and the adsorption energy was analyzed using density functional theory. The results show that the adsorption of H2O molecules on perfect and Fe/Al-substituted dolomites is weak chemisorption, and the Fe and Al impurities weaken and enhance the adsorption capacity of H2O molecules, respectively. Therefore, the hydrophilicity of the dolomite surface increases in the following order: Fe-substituted dolomite < perfect dolomite < Al-substituted dolomite. The Mulliken charge and bond group analysis shows that the adsorption of H2O molecules on dolomite is primarily through the interaction between Ow and Ca atoms, where the d orbitals of Ca atoms provide charges for Ow atoms to form ionic bonds, which related to the poor electronegativity of Ca atoms and their weak valence electron binding ability. The DOS analysis shows that, during the adsorption of H2O molecules on dolomite, Mg and Al atoms have less influence on the dolomite surface, whereas Fe and Ca atoms undergo competitive adsorption, which inhibits the interaction between Ca atoms and H2O molecules on the dolomite surface

Nanopolymers Delivery of the Bone Morphogenetic Protein-4 Plasmid to Mesenchymal Stem Cells Promotes Articular Cartilage Repair In Vitro and In Vivo

The clinical application of viral vectors for gene therapy is limited for biosafety consideration. In this study, to promote articular cartilage repair, poly (lactic-co glycolic acid) (PLGA) nanopolymers were used as non-viral vectors to transfect rabbit mesenchymal stem cells (MSCs) with the pDC316-BMP4-EGFP plasmid. The cytotoxicity and transfection efficiency in vitro were acceptable measuring by CCK-8 and flow cytometry. After transfection, Chondrogenic markers (mRNA of Col2a1, Sox9, Bmp4, and Agg) of experimental cells (MSCs being transfected with BMP-4 plasmid by PLGA nanopolymers) were increased more than those of control cells (MSCs being transfected with naked BMP-4 plasmid alone). In vivo study, twelve rabbits (24 knees) with large full thickness articular cartilage defects were randomly divided into the experimental group (MSCs being transfected with BMP-4 plasmid by PLGA nanopolymers) and the control group (MSCs being transfected with naked BMP-4 plasmid). The experimental group showed better regeneration than the control group 6 and 12 weeks postoperatively. Hyaline-like cartilage formed at week 12 in the experimental group, indicating the local delivery of BMP-4 plasmid to MSCs by PLGA nanopolymers improved articular cartilage repair significantly. PLGA nanopolymers could be a promising and effective non-viral vector for gene therapy in cartilage repair

A Review of Molten Salt Reactor Multi-Physics Coupling Models and Development Prospects

Molten salt reactors (MSRs) are one type of GEN-IV advanced reactors that adopt melt mixtures of heavy metal elements and molten salt as both fuel and coolant. The liquid fuel allows MSRs to perform online refueling, reprocessing, and helium bubbling. The fuel utilization, safety, and economics can be enhanced, while some new physical mechanisms and phenomena emerge simultaneously, which would significantly complicate the numerical simulation of MSRs. The dual roles of molten fuel salt in the core lead to a tighter coupling of physical mechanisms since the released fission energy will be absorbed immediately by the molten salt itself and then transferred to the primary heat exchanger. The modeling of multi-physics coupling is regarded as one important aspect of MSR study, attracting growing attention worldwide. Up to now, great efforts have been made in the development of MSR multi-physics coupling models over the past 60 years, especially after 2000, when MSR was selected for one of the GEN-IV advanced reactors. In this paper, the development status of the MSR multi-physics coupling model is extensively reviewed in the light of coupling models of N-TH (neutronics and thermal hydraulics), N-TH-BN (neutronics, thermal hydraulics, and burnup) and N-TH-BN-G (neutronics, thermal hydraulics, burnup, and graphite deformation). The problems, challenges, and development trends are outlined to provide a basis for the future development of MSR multi-physics coupling models

In Vivo Study of Ligament-Bone Healing after Anterior Cruciate Ligament Reconstruction Using Autologous Tendons with Mesenchymal Stem Cells Affinity Peptide Conjugated Electrospun Nanofibrous Scaffold

Electrospinning nanofibrous scaffold was commonly used in tissue regeneration recently. Nanofibers with specific topological characteristics were reported to be able to induce osteogenic differentiation of MSCs. In this in vivo study, autologous tendon grafts with lattice-like nanofibrous scaffold wrapping at two ends of autologous tendon were used to promote early stage of ligament-bone healing after rabbit ACL reconstruction. To utilize native MSCs from bone marrow, an MSCs specific affinity peptide E7 was conjugated to nanofibrous meshes. After 3 months, H-E assessment and specific staining of collagen type I, II, and III showed direct ligament-bone insertion with typical four zones (bone, calcified fibrocartilage, fibrocartilage, and ligament) in bioactive scaffold reconstruction group. Diameters of bone tunnel were smaller in nanofibrous scaffold conjugated E7 peptide group than those in control group. The failure load of substitution complex also indicated a stronger ligament-bone insertion healing using bioactive scaffold. In conclusion, lattice-like nanofibrous scaffold with specific MSCs affinity peptide has great potential in promoting early stage of ligament-bone healing after ACL reconstruction

Metformin Sensitizes Leukemia Cells to Vincristine via Activation of AMP-activated Protein Kinase

Vincristine is extensively used chemotherapeutic medicine to treat leukemia. However, it remains a critical clinical problem with regard to its toxicity and drug-resistance. AMP-activated protein kinase (AMPK) is an energy sensor that is pivotal in maintaining cell metabolic homeostasis. It is reported that AMPK is involved in vincristine-induced apoptosis. However, whether AMPK is involved in chemotherapy-resistance is largely unclear. It is well-documented that metformin, a widely used medicine to treat type II diabetes, possesses anti-cancer activities, yet whether metformin affects leukemia cell viability via vincristine is unknown. In this study, we showed that both AMPKα1 mRNA and phosphorylated AMPK protein levels were significantly decreased in clinical leukemia samples. We further demonstrated that metformin sensitized leukemia cells to vincristine-induced apoptosis in an AMPK-dependent manner. In addition, knockdown of AMPKα1 significantly reduced the effects of metformin on vincristine-induced apoptosis. Taken together, these results indicate that AMPK activation is critical in metformin effects on vincristine-induced apoptosis and suggest a putative strategy of a combination therapy using metformin and vincristine in treatment of leukemia

Exploring the Impact of Short Term Travel on Gut Microbiota and Probiotic Bacteria Mediated Stability

Although travelers are frequently accompanied by abdominal discomfort and even diarrhea, not every trip can cause this issue. Many studies have reported that intestinal microbes play an important role in it. However, little is known about the reason for the dynamics of these intestinal microbes. Here, we delved into the effects of short-term travel on the gut microbiota of 12 healthy individuals. A total of 72 fecal samples collected before and after one-week travel, alongside non-traveling controls, underwent amplicon sequencing and a series of bioinformatic analyses. We found that travel significantly increased intra-individual gut microbiota fluctuations without diarrhea symptoms. In addition, the initial composition of the gut microbiota before travel emerged as a crucial factor in understanding these fluctuations. Travelers with stable microbiota exhibited an enrichment of specific probiotic bacteria (Agathobaculum, Faecalibacterium, Bifidobacterium, Roseburia, Lactobacillus) before travel. Another batch of data validated their predictive role in distinguishing travelers with and without the gut microbial disorder. This work provided valuable insights into understanding the relationship between gut microbiota and travel. It offered a microbiota-centric perspective and a potential avenue for interventions to preserve gut health during travel

Detection of ADAMTS‑4 Activity Using a Fluorogenic Peptide-Conjugated Au Nanoparticle Probe in Human Knee Synovial Fluid

A disintegrin and metalloproteinase with thrombospondin motif-4 (ADAMTS-4) plays a pivotal role in degrading aggrecan, which is an early event in cartilage degrading joint diseases such as osteoarthritis (OA). Detection of ADAMTS-4 activity could provide useful clinical information for early diagnosis of such diseases and disease-modifying therapy. Therefore, we developed a ADAMTS-4 detective fluorescent turn-on AuNP probe (ADAMTS-4-D-Au probe) by conjugating gold nanoparticles with a FITC-modified ADAMTS-4-specific peptide (DVQEFRGVTAVIR). When the ADAMTS-4-D-Au probe was incubated with ADAMTS-4, the fluorescence recovered and fluorescence intensity markedly increased in proportion to concentrations of ADAMTS-4 and the probe. A nearly 3-fold increase in fluorescent intensity in response to only 3.9 pM of ADAMTS-4 was detected, whereas almost no fluorescence recovery was observed when the probe was incubated with matrix metalloproteinase (MMP)-1, -3, and -13. These results indicate a relative high sensitivity and specificity of the probe. Moreover, ADAMTS-4-D-Au probe was used to detect ADAMTS-4 activity in synovial fluid from 11 knee surgery patients. A substantial increase in fluorescent intensity was observed in the acute joint injury group as compared to the chronic joint injury and end-stage OA groups, indicating that this simple and low-cost sensing system might serve as a new detection method for ADAMTS-4 activity in biological samples and in screens for inhibitors for ADAMTS-4-related joint diseases. Additionally, this probe could be a potential biomarker for early diagnosis of cartilage-degrading joint diseases