Molecular Biotechnology最新文献

Autophagy regulates intermittent hypoxia (IH)-induced obstructive sleep apnea-hypopnea syndrome (OSAHS). We investigated the effects of IH and its withdrawal on cognitive function, autophagy, and lysophagy in OSAHS. An OSAHS rat model was established, and rats were divided into five groups: normoxia control, IH-4w (4-week IH), IH-6w (6-week IH), IH-8w (8-week IH), and IH-8w + 4w (8-week IH and 4-week normoxia). The cognitive behavior; mitochondrial and lysosomal morphology of the hippocampal tissue; mitochondrial respiratory function, permeability, and membrane potential; lysosomal function; autophagy- and lysophagy-related protein levels; and hypoxia-associated autophagy gene expression in rats were assessed. The cognitive function of rats in the IH-4w, IH-6w, and IH-8w groups was significantly impaired. In IH-8w cells, mitochondrial function was damaged with swollen morphology and decreased quantity, respiration, permeability, and membrane potential, along with significantly increased mitophagy-related protein ATG5 and LC3II/LC3 levels and decreased p62 levels. Expression of hypoxia-associated autophagy genes Becn1, Hif1, Bnip3, Bnip3l, and Fundc1 was significantly higher in the IH-8w group. Significantly increased LAMP2, CTSB, and ACP2 levels in IH-8w cells further indicated impaired lysosomal function. Lysophagy-related protein LAMP1, LC3II/LC3I, and TFEB levels were significantly increased in the IH-8w group, whereas p62 level was significantly decreased. The above listed evidence indicated damage to the mitochondria and lysosomes, as well as stimulation of mitophagy and lysophagy in IH-treatment OSAHS rat model. After withdrawing IH and culturing for 4 weeks in normal conditions, the cognitive function of rats improved, and mitophagy and lysophagy decreased. Our findings indicate that IH impairs cognitive function and promotes mitophagy and lysophagy in an OSAHS rat model, and IH withdrawal recovered the above effects.

Breast cancer has emerged as the primary cause of mortality stemming from malignancies among women. HuaChanSu has demonstrated efficacy in suppressing the progression of various malignancies. However, the specific immune targets and pathways influenced by HuaChanSu within mammary tumors remain elusive. This study is designed to uncover potent monomers and pivotal targets associated with HuaChanSu's anti-breast cancer Immunotherapy. The genes pertinent to HuaChanSu and breast cancer were acquired individually from publicly available databases. Interaction analysis using Cytoscape was conducted on common genes to determine the most suitable targets and crucial constituents of HuaChanSu's Immunotherapy against breast cancer. Following this, molecular docking was employed to validate ligand and receptor binding interactions. Lastly, the identified core genes underwent assessment of immune infiltration. The intersection of HuaChanSu and BC targets yielded a total of 49 differentially expressed genes. Bufalin emerged as the most potent constituent in Immunotherapy. Immunoassay data demonstrated significant correlations (r > 0.03, p < 0.05) between S100B, MMP9, FOS, EGFR, KIT, MME, and immune infiltration within BC. Molecular docking further corroborated the effective binding of Bufalin with immune-related genes. Through network pharmacological validation, we propose the extraction of Bufalin, a monomeric constituent of Huachansu, to exert immunomodulatory effects aimed at inhibiting the progression of breast cancer. Most of the target genes (S100B, BIRC5, MMP9, FOS, EGFR, KIT, and MME) are common targets for immunotherapy.

Breast cancer dominates women's mortality, and among other factors, mutations in the BRCA1 gene are significant risk factors. Several approaches are followed to treat the BRCA1 affected cancer patients. However, specific BRCA1 inhibitors are not available till date due to its structural complexity. In addition, there are several limitations associated with the existing drugs used to treat BRCA1-related breast cancer and some side effects. The side effects include symptoms such as hot flashes, joint pain, nausea, fatigue, hair loss, diarrhea, chills, fever, and others. Therefore, advanced approaches needed that can overcome all the limitations and side effects of the current inhibitors. In this study, we adopted a multistep approach to identify potential inhibitors for BRCA1-mutated breast cancer. We used our developed machine learning models to screen potential inhibitors. Molecular docking approach was carried out for the screened hit compounds with BRCA1 and its mutated forms. Two ligands, β-amyrin and Narirutin, has shown significant performance in multiple scoring schemes such as molecular docking and RF score calculations. Molecular dynamics simulations demonstrated the stability of the complexes formed by β-amyrin and Narirutin with BRCA1, with lower RMSD values and less RMSF fluctuations at the binding site locations. Principal component analysis (PCA) and free energy landscape (FEL) further confirmed the compactness and favorable binding of β-Amyrin and Narirutin to BRCA1. These findings suggest that β-amyrin and Narirutin have potential as therapeutic agents against BRCA1-mutated breast cancer.

The study aimed to explore the potential of QiangJin mixture (QJM), a Chinese herbal compound prescription, in regulating MC3T3-E1 cell differentiation and to analyze the ingredients and therapeutic targets of QJM against osteoporosis based on network pharmacology. MC3T3-E1 cells were incubated with different concentrations of QJM-contained rat serum (5, 10, or 20%). After 14 days of cell culture, Alizarin Red staining was performed to assess the mineralization ability of osteoblasts. RT-qPCR was used to measure mRNA levels of osteogenesis-related genes. Western blot was conducted to measure protein levels of factors related to the BMP2/Smads pathway. Functional and pathway enrichment of overlapping targets for QJM and osteoporosis were analyzed using gene ontology and KEGG analyses. As shown by experimental results, QJM-contained serum led to calcium deposition, increased expression levels of osteogenesis-related genes, and activated BMP2/Smad/Runx2 signaling in MC3T3-E1 cells. A total of 125 active compounds and 162 disease-related targets were identified. The core targets were MAPK8, TP53, ESR1, STAT3, MAPK3, IL6, NFKB1, JUN, MAPK1 and AKT1. In conclusion, QJM promotes the osteogenic differentiation of MC3T3-E1 cells by activating the BMP2/Smads signaling. Additionally, QJM is an anti-osteoporotic mixture by regulating diverse therapeutic targets and signaling pathways.

To discover the molecular mechanism of Astragaloside IV (AS IV) in PM2.5-induced lung injury and pulmonary fibrosis (PF). A lung injury rat model was induced by PM2.5 and injected intraperitoneally with AS IV. Lungs were harvested to evaluate lung tissue injury and apoptosis. Rat alveolar epithelial cells L2 were exposed to PM2.5 and treated with AS IV. After cellular transfection, cell proliferation, LDH production, and apoptosis were measured. In both models, inflammatory factors and fibrotic indices were measured by ELISA and Western blot. miR-362-3p and RUNX1 interplay was explored and confirmed. Administration of AS IV attenuated PM2.5-induced lung tissue injury, inflammation, apoptosis, and PF in rats. AS IV enhanced proliferation and reduced LDH release, apoptosis, inflammation, and PF in PM2.5-treated L2 cells. MiR-362-3p upregulation improved PM2.5-induced L2 cell injury. AS IV improved PM2.5-induced lung injury by upregulating miR-362-3p. miR-362-3p had an inhibition effect on RUNX1 expression. RUNX1 upregulation weakened the therapeutic effect of AS IV on PM2.5-induced alveolar epithelial cell injury. AS IV inhibits lung injury and PF induced by PM2.5 by targeting RUNX1 through upregulation of miR-362-3p.

Microbial infections pose a substantial global health challenge, particularly impacting immunocompromised individuals and exacerbating the issue of antimicrobial resistance (AMR). High virulence of pathogens can lead to severe infections and prolonged antimicrobial treatment, increasing the risk of developing resistant strains. Integrating machine-learning (ML) with DNA sequencing technologies offers potential solutions by enhancing microbial identification, virulence assessment, and antimicrobial susceptibility evaluation. This review explores recent advancements in these integrated approaches, addressing current limitations and identifying gaps in the literature. A comprehensive literature search was conducted across databases including PubMed, Scopus, Web of Science, and IEEE Xplore, covering publications from January 2014 to June 2024. Using a detailed Boolean search string, relevant studies focusing on ML applications in microorganism identification, antimicrobial susceptibility testing, and microbial virulence were included. The screening process involved a two-stage review of titles, abstracts, and full texts, with data extraction and critical appraisal performed using the QIAO tool. Data were analyzed through narrative synthesis to identify common themes and innovations. Out of 1,650 initially identified records, 19 studies met the inclusion criteria. These studies primarily focused on AMR, with additional research on microbial virulence and identification. Machine learning algorithms such as Random Forest, Support Vector Machines, and Convolutional Neural Networks, combined with DNA sequencing techniques like Whole Genome Sequencing and Metagenomic Sequencing, demonstrated significant advancements in predictive accuracy and efficiency. High-quality studies achieved impressive performance metrics, including F1-scores up to 0.88 and AUC scores up to 0.96. The integration of ML and DNA sequencing technologies has significantly enhanced microbial analysis, improving the identification of pathogens, assessment of virulence, and evaluation of antimicrobial susceptibility. Despite advancements, challenges such as data quality, high costs, and model interpretability persist. This review highlights the need for continued innovation and provides recommendations for future research to address these limitations and improve disease management and public health strategies. The systematic review is registered with PROSPERO (CRD42024571347).

The promotive effect of P53 apoptosis effector related to PMP-22 (PERP) on lung adenocarcinoma (LUAD) has been confirmed. However, the N6-methyladenosine (m6A) modification of PERP to regulate LUAD progression have not been revealed. Bioinformatic analysis predicted the mechanism of PERP interacting with RBM15 and p53 pathway using GEPIA and The Cancer Genome Atlas (TCGA) databases. The qRT-PCR, cell function experiments, and western blotting were applied to further confirm the function and mechanism of PERP and RBM15 in LUAD cells. Methylated RNA immunoprecipitation (MeRIP) and mRNA stability assays were used to reveal the interaction between PERP and RBM15 in LUAD cells. PERP with high expression in LUAD showed the poor survival. Silencing PERP prevented LUAD cells to proliferate, migrate, and invade via activating p53 pathway, whereas overexpressing PERP showed the opposite effect on LUAD cells. Mechanistically, RBM15 overexpression could promote PERP m6A modification to enhance the PERP mRNA stability. In addition, RBM15 overexpression leading to LUAD cell malignancy was reversed by PERP knockdown. This study reveals that the m⁶A modification of PERP regulated by RBM15 enhances the tumorigenesis of LUAD by inhibiting the p53 signaling pathway, which may provide novel insights into the LUAD mechanism.

Porcine circovirus type 2 (PCV2) is a pervasive pathogen in the swine industry, leading to a spectrum of disorders known as porcine circovirus associated diseases (PCVAD). The PCV2 Cap protein contains critical antigenic epitopes and is the primary target for vaccine development. Current vaccines include inactivated viral particles and virus-like particles (VLPs), with experimental vaccines exploring various innovative approaches. This study introduces a novel Golden Gate assembly-based, Escherichia coli expression destination plasmid, pPRSVCP-E18, designed for the in-frame insertion of short peptide-coding DNA sequences into a highly antigenic site of Papaya ringspot virus (PRSV) coat protein (CP). We successfully cloned four PCV2 Cap peptides into this plasmid, expressed the chimeric CP proteins in E. coli under flask and bioreactor conditions, and assembled them into VLPs. These VLPs, when adjuvated and administered to BALB/c mice, elicited a specific IgG response against the PCV2 Cap peptides. Our findings demonstrate the plasmid's high efficiency for Golden Gate cloning and its potential in developing subunit vaccines against PCV2, contributing to the sustainable control of PCVAD in the swine industry.

Short non-coding ribonucleic acids are also known as "Micro ribonucleic acids (miRNAs)". The miRNAs make a contribution to the regulation of genes and mitigation of cancer cell growth in humans. miRNAs play a significant role in several BPs, namely apoptosis, cell cycle progression, and development. It is well-recognized that miRNAs are crucial for the tumors' growth and also serve as Tumor Suppressors (TSs) or oncogenes. As miRNAs also act as an effective tumor suppressor, studying the molecular diversities of the miRNAs makes way to minimize cancer progression and the corresponding death rates in the future. Therefore, miRNAs along with their Biological Processes (BPs) and molecular diversities are thoroughly researched in this paper. Consequently, miRNAs particularly target their 3' UnTranslated Region (3'-UTR) for controlling the target mRNAs' stability and protein translation. So, this study also expresses the impact of microRNA variants in various cancer cells, namely Breast cancer, Gastric or stomach cancer, ovarian cancer, and lymphocytic leukemia. Furthermore, the database named PhenomiR and commercial kits that are used in the miRNA data analysis are discussed in this article to provide extensive knowledge about the molecular diversity analysis of miRNA and their influences on cancerous cells.

Whether it involves human subjects or non-human animals, basic, translational, or clinical sleep research poses significant ethical challenges for researchers and ethical committees alike. Sleep research greatly benefits from using diverse animal models, each offering unique insights into sleep control mechanisms. The fruit fly (Drosophila melanogaster) is a superior genetic model due to its quick generation period, large progenies, and rich genetic tools. Its well-characterized genome and ability to respond to hypnotics and stimulants make it an effective tool for studying sleep genetics and physiological foundations. The nematode (Caenorhabditis elegans) has a simpler neural organization and transparent body, allowing researchers to explore molecular underpinnings of sleep control. Vertebrate models, like zebrafish (Danio rerio), provide insights into circadian rhythm regulation, memory consolidation, and drug effects on sleep. Invertebrate models, like California sea hare (Aplysia californica) and Upside-down jellyfish (Cassiopea xamachana), have simpler nervous systems and behave similarly to humans, allowing for the examination of sleep principles without logistical and ethical challenges. Combining vertebrate and invertebrate animal models offers a comprehensive approach to studying sleep, improving our understanding of sleep regulation and potentially leading to new drug discovery processes for sleep disorders and related illnesses.