Molecular Biotechnology最新文献

Pyrethrins are powerful natural insecticides traditionally extracted from the flowers of Tanacetum cinerariifolium. While effective and environmentally friendly, their agricultural production is limited by genetic variability, environmental factors, and labor-intensive cultivation. Advances in understanding the pyrethrin biosynthetic pathway, including the discovery and heterologous synthesis of key enzymes, have created new opportunities to rethink production methods. This review covers current knowledge of pyrethrin biosynthesis, focusing on precursor pathways and the challenges that hinder their heterologous production. We also discuss the remaining gaps and how synthetic biology and metabolic engineering can solve these issues. By shifting the focus from traditional flower farming to engineered cell factories, we suggest a new approach for achieving scalable, consistent, and sustainable pyrethrin production.

To deeply investigate the mechanism of ferroptosis-related genes in the process of bone nonunion based on the GEO database. And using Mendelian randomization to explore the causal association of 15 trace elements with the occurrence of bone nonunion. Bone nonunion RNA-seq data were retrieved and downloaded from the GEO database. The differentially expressed genes in bone nonunion were identified using two differential expression analysis methods, "limma" and "WGCNA". Random Forest Tree, Support Vector Machine, and Lasso-cox were used to analyze and screen the genes related to ferroptosis in bone nonunion; A risk model of bone nonunion was constructed based on the screened ferroptosis-related genes; based on this, the pathway mechanism of ferroptosis-related genes involved in the occurrence and development of bone nonunion was further investigated. Mendelian randomization analysis was performed using inverse variance weighting as the main analysis method, and weighted median, Weighted mode, Mr-Egger, and Simple mode were used as complementary methods. Heterogeneity was detected using Cochran's Q test and funnel plot analysis, horizontal pleiotropy was detected using Mr-Egger intercept, and sensitivity analyses were performed using the "leave-one-out" method. PTGS2/PRKCA/MAPK14 all showed excellent diagnostic efficacy for bone nonunion. The risk prediction model based on PTGS2, PRKCA, and MAPK14 showed good predictive efficacy and clinical benefit rate for bone nonunion. Ferroptosis core gene PRKCA may be involved in the VEGF signaling pathway to affect the cell cycle and inhibit fracture healing. MR analysis suggests that Potassium and Vitamin E are protective factors for the development of bone nonunion. Ferroptosis genes PTGS2/PRKCA/MAPK14 are potential diagnostic targets for bone nonunion. The down-regulation of PRKCA expression may inhibit fracture healing through the VEGF signaling pathway during the growth of blood vessels at fracture breaks. The results of MR suggested that Potassium and Vitamin E have a promoting effect on fracture healing.

Perinatal white matter injury (WMI), which is prevalent in premature infants, involves M2 microglia affecting oligodendrocyte precursor cells (OPCs) through exosomes, promoting OPC growth and reducing WMI. The molecular mechanism of WMI remains unclear, and this study explored the role of M2 microglia-derived exosomes in WMI. A tMCAO rat model was constructed to simulate WMI characteristics in vivo. Cresyl violet staining, neurobehavioral tests, rotarod tests, immunofluorescence and immunochemistry were used to assess the role of exos-derived miR-144-5p in pathological and neurological changes in rats. OGD/R cellular models were constructed to mimic WMI characteristics in vitro. CCK-8, TUNEL, Western blotting and immunofluorescence were used to assess the role of exos-derived miR-144-5p in OPC phenotypes. Rescue assays were used to assess the role of the PTEN/AKT pathway in miR-144-5p-mediated OPC phenotypes. Bioinformatics and mechanistic experiments were used to assess the association of PTEN or KLF12 with miR-144-5p in OPCs. M2-Exos suppressed cerebral injury and facilitated demyelination repair in rats post WMI. M2-Exos suppressed OGD/R-stimulated OPC apoptosis and facilitated OGD/R-stimulated OPC differentiation. M2-Exo-derived miR-144-5p suppressed OGD/R-stimulated OPC apoptosis and facilitated OGD/R-stimulated OPC differentiation. M2-Exo-derived miR-144-5p suppressed cerebral injury and facilitated demyelination repair in rats post WMI. MiR-144-5p suppressed OGD/R-stimulated OPC apoptosis and facilitated OGD/R-stimulated OPC differentiation through PTEN downregulation. MiR-144-5p targeted the KLF12 3'UTR to repress PTEN transcription in OPCs. M2 microglia secrete miR-144-5p to reduce WMI by targeting KLF12 in OPCs, inhibiting PTEN/AKT pathway activity, and offering potential targeted therapeutic insights for WMI.

Buffaloes play a crucial role in Asian agriculture, enhancing food security and rural development. Their distinct metabolic needs drive tissue-specific mitochondrial adaptations, regulated by both mitochondrial and nuclear genomes. This study explores how nuclear-encoded mitochondrial genes involved in lipid and carbohydrate metabolism vary across tissues-an area with significant implications for buffalo health, productivity, and human health. We hypothesize that tissue-specific variations in metabolic pathways are reflected in the expression of nuclear-encoded mitochondrial genes, which are tailored to the metabolic needs of each tissue. We utilized high-throughput RNA sequencing (RNA-seq) data to assess the expression of nuclear-encoded mitochondrial genes related to lipid and carbohydrate metabolism across various tissues in healthy female buffaloes aged 3-5 years, including the kidney, heart, brain, and ovary. Differential expression analysis was performed using DESeq2, with significance set at p < 0.05 for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. A total of 164 genes exhibited tissue-specific regulation, with the heart and brain, which have higher energy demands, expressing more genes than the kidney and ovary. Notably, the comparison between the kidney and ovary showed the highest number of differentially expressed genes. Interestingly, the kidney up-regulates gluconeogenesis-related genes (e.g., PCK2, PCCA, LDHD), promoting glucose production, while these genes are down-regulated in the ovary. In contrast, the brain up-regulates pyruvate metabolism genes (e.g., PCCA, PDHA1, LDHD), underscoring its reliance on glucose as a primary energy source, while these genes are down-regulated in the ovary. The higher abundance of EHHADH in the brain compared to the ovary further emphasizes the critical role of fatty acid metabolism in brain function, aligned with the brain's high energy demands. Additionally, down-regulation of the StAR gene in both the kidney versus ovary and brain versus ovary comparisons suggests tissue-specific differences in steroid hormone regulation. These findings highlight tissue-specific variations in nuclear-encoded mitochondrial genes related to lipid and carbohydrate metabolism, reflecting adaptations to each tissue's unique metabolic needs. This study lays a foundation for advancing mitochondrial metabolism research in livestock, with significant implications for human health. Insights could inform dietary or therapeutic strategies for metabolic disorders, such as cardiovascular diseases and metabolic syndrome, while also enhancing livestock productivity.

Opioids are the primary regimens for perioperative analgesia with controversial effects on oncological survival. The underlying mechanism remains unexplored. This study developed survival-related gene co-expression networks based on RNA-seq and clinical characteristics from TCGA cohort. Two survival-related networks were identified, and drug-induced transcriptional profiles were predicted. Immune cell infiltration algorithm, least absolute shrinkage and selection operator (LASSO) regression, and cox proportional models were executed to explore the correlation between opioid-related drugs and prostate cancer patient prognosis. The opioid receptor agonists, represented by tramadol, were evidenced for anti-survival effects on prostate cancer by facilitating the DNA replication and cell cycle, and immune cell infiltration. Conversely, opioid receptor antagonists showed pro-survival effects. A novel prognostic model containing CNIH2, MCCC1, and Gleason scores was established and validated in two independent cohorts. This study revealed opioids' effect on prostate cancer progression, and provided a novel model to predict these regulations in clinical outcomes.

Antibodies have specific binding capabilities and therapeutic potential for treating various diseases, including viral infections. The amino acid composition of the hypervariable complementarity determining regions (CDR) loops and the framework regions (FR) are the determining factors for the affinity and therapeutic efficacy of the antibodies. In this study selected and curated, 77 viral antigen-human antibody complexes from Protein data bank from the Thera-SAbdab database were analyzed. The results revealed diversity indices within specific CDR regions, amino acid frequencies, paratope-epitope interactions, bond formations, and bond types among the analyzed viral Ag-Ab complexes. The finding revealed that Ser, Gly, Tyr, Thr, and Phe are prominently present in the antibody CDRs. Analysis of CDR profiles indicated an average amino acid diversity of 60-80% in heavy chain CDRs and 45-60% in light chain CDRs. Aromatic residues, particularly Tyr, Phe, and Trp showed significant involvement in the paratope-epitope interactions in the heavy chain, while Tyr, Ser, and Thr were key contributors in the light chain. Furthermore, the study examined the occurrence of amino acids in both light and heavy chains of viral Ag- human Ab complexes, analyzing the presence of amino acids as single residues, dipeptides and tripeptides. The analysis is crucial for enhancing the antibody engineering processes including, design, optimization, affinity enhancement, and overall antibody development.

Nucleolin (NCL) is a prevalent and widely distributed nucleolar protein in cells. While primarily located in the nucleolus, NCL is also found within the nucleoplasm, cytoplasm, and even on the cell surface. NCL's unique nature arises from its multifaceted roles and extensive interactions with various proteins. The structural stability of NCL is reliant on protease inhibitors, particularly in proliferating cells, indicating its essential role in cellular maintenance. This review is centered on elucidating the structure of NCL, its significance in host-viral interactions, and its various contributions to viral progeny production. This work is to enhance the scientific community's understanding of NCL functionality and its implications for viral infection processes. NCL is highlighted as a crucial host protein that viruses frequently target, exploiting it to support their own life cycles and establish infections. Understanding these interactions is key to identifying NCL's role in viral pathogenesis and its potential as a therapeutic target. Our current knowledge, alongside extensive scientific literature, underscores the critical role of host proteins like NCL in both viral infections and other diseases. As a target for viral exploitation, NCL supports viral replication and survival, making it a promising candidate for therapeutic intervention. By delving deeper into the intricacies of NCL-viral protein interactions, researchers may uncover effective antiviral mechanisms. This review aspires to inspire further research into NCL's role in viral infections and promote advancements in antiviral therapeutic development.

Clustered, regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) system is a new gene editing tool that represents a revolution in gene therapy. This study aimed to review the clinical trials conducted to evaluate the efficacy and safety of the CRISPR/Cas9 system in treating thalassemia and sickle cell disease (SCD). We searched relevant literature using "CRISPR Cas", "thalassemia", "sickle cell" and "clinical trial" as subject terms in PubMed, Cochrane, Web of Science, and Google Scholar up to December 3rd, 2023. Following the PIO format (Patients, Intervention, Outcome), PRISMA guidelines were followed in the study selection, data extraction, and quality assessment processes. Out of 110 publications, 6 studies met our eligibility criteria with a total of 115 patients involved. CRISPR/Cas9 system was used to disrupt BCL11A gene enhancer in 4 studies and to disrupt γ-globin gene promoters in 2 studies. Patients demonstrated significant activation of fetal hemoglobin, elevated total hemoglobin, transfusion independence in thalassemia, and repression of vaso-occlusive episodes in SCD. Using CRISPR/Cas9 system to directly disrupt genes provides a safe and potential one-time functional cure for thalassemia and SCD, suggesting CRISPR/Cas9 as a potential therapeutic tool for the treatment of inherited hematological disorders.

The etiological agent for the coronavirus disease 2019 (COVID-19), the SARS-CoV-2, caused a global pandemic. Although mRNA, viral-vectored, DNA, and recombinant protein vaccine candidates were effective against the SARS-CoV-2 Wuhan strain, the emergence of SARS-CoV-2 variants of concern (VOCs) reduced the protective efficacies of these vaccines. This necessitates the need for effective and accelerated vaccine development against mutated VOCs. The development of multi-epitope vaccines against SARS-CoV-2 based on in silico identification of highly conserved and immunogenic epitopes is a promising strategy for future SARS-CoV-2 vaccine development. Considering the evolving landscape of the COVID-19 pandemic, we have conducted a bibliometric analysis to consolidate current findings and research trends in multi-epitope vaccine development to provide insights for future vaccine development strategies. Analysis of 102 publications on multi-epitope vaccine development against SARS-CoV-2 revealed significant growth and global collaboration, with India leading in the number of publications, along with an identification of the most prolific authors. Key journals included the Journal of Biomolecular Structure and Dynamics, while top collaborations involved Pakistan-China and India-USA. Keyword analysis showed a prominent focus on immunoinformatics, epitope prediction, and spike glycoprotein. Advances in immunoinformatics, including AI-driven epitope prediction, offer promising avenues for the development of safe and effective multi-epitope vaccines. Immunogenicity may be further improved through nanoparticle-based systems or the use of adjuvants along with real-time genomic surveillance to tailor vaccines against emerging variants.

Androgen deprivation therapy (ADT) is the primary treatment strategy for prostate cancer. However, despite an initially favorable response, tumors inevitably progress to castration-resistant prostate cancer (CRPC). Therefore, the exploration of new therapeutic approaches targeting CRPC has become imperative. Increasing evidence suggests that hypoxia plays a crucial role in the development of CRPC. In this study, we found that the emergence of alkaliptosis resistance and the expression of its marker, CA9, significantly contribute to the progression of castration resistance induced by hypoxia. This study utilized bioinformatics approaches to identify genetic determinants associated with alkaliptosis resistance and explored the clinical significance of these marker genes. Transcriptomic sequencing was performed on the DU145 prostate cancer cell line, which had been induced to acquire alkaliptosis resistance. Using least absolute shrinkage and selection operator (LASSO) regression analysis, a prognostic risk model consisting of 12 genes, including ADORA2A, KCNG4, SEC14L5, B3GAT2, SLFNL1, FAM72D, CBWD3, PPM1K, STARD4, DEPDC1B, MATN3, and DDIAS was developed. The risk model score demonstrated a strong correlation with key patient clinical characteristics, including Gleason score, PSA levels, T stage, and N stage, and was also associated with immune therapy response and biochemical recurrence-free survival (BCRFS). Furthermore, ADORA2A expression in cellular models was found to be a critical factor in promoting alkaliptosis resistance.