Predicting potential DNA binding motifs is a critical part of understanding gene expression across all domains of life. Here, we report the development of Delila-PY, an easy-to-use pipeline for utilizing the Delila suite of software to identify DNA binding motifs.
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http://dx.doi.org/10.1128/MRA.00160-21 | DOI Listing |
Trends Biotechnol
March 2025
Tidetron Bioworks Technology (Guangzhou) Co., Ltd, Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong 510000, PR China. Electronic address:
Targeted random mutagenesis is crucial for breeding, directed evolution, and gene function studies, yet efficient tools remain scarce. Here, we present obligate mobile element guided activity (OMEGA)-R, an innovative targeted random mutagenesis system that integrates SpyCatcher-enIscB and PolI3M-TBD-SpyTag, outperforming existing state-of-the-art technologies in key metrics, such as protein size, mutagenesis efficiency, window length, and continuity. OMEGA-R achieves a dramatic enhancement of on-target mutagenesis, reaching a rate of 1.
View Article and Find Full Text PDFTrends Biotechnol
March 2025
Department of Bioengineering, Imperial College London, London, UK; Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
Building DNA constructs of increasing complexity is key to synthetic biology. Golden Gate (GG) methods led to the creation of cloning toolkits - collections of modular standardized DNA parts hosted on hierarchic plasmids, developed for yeast, plants, Gram-negative bacteria, and human cells. However, Gram-positive bacteria have been neglected.
View Article and Find Full Text PDFInt J Biol Macromol
March 2025
Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China. Electronic address:
In recent years, the phenomenon of zinc pollution in orchards has become increasingly serious, and the safety of apple production is facing a major risk. Therefore, exploring excellent genes for zinc tolerance has a positive effect on apples. Up to now, there is still a lack of attention on genes related to zinc stress tolerance in apples.
View Article and Find Full Text PDFJ Immunol
January 2025
Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei City, Taiwan.
Decoy receptor 3 (DcR3), a soluble receptor in the tumor necrosis factor receptor superfamily, regulates the functions of monocytes, macrophages, dendritic cells, and T cells. Previous studies have demonstrated that DcR3 suppresses B cell proliferation in vitro and ameliorates autoimmune diseases in animal models; however, whether and how DcR3 regulates antibody production is unclear. Using a DcR3 transgenic mouse model, we found that DcR3 impaired the T cell-dependent antigen-stimulated antibody response.
View Article and Find Full Text PDFJ Immunol
February 2025
Division of Pulmonary, Critical Care and Sleep Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.
The erythroblastic island (EBI) functions as a niche in which erythroblastic island macrophages (EBIMφs) are positioned within rings of erythroblasts, providing support and signals that orchestrate efficient erythropoiesis. We postulated burn injury impacts the EBI niche, given the nearly universal presence of anemia and inflammation in burn patients, and a divergent myeloid transcriptional signature that we observed in murine bone marrow following burn injury, in which granulocyte colony-stimulating factor (G-CSF) secretion broadly attenuated the expression of EBIMφ marker genes. Notably, we identified the heme-induced transcription factor Spi-C as a robust marker of EBIMφs in Spicigfp/igfp mice.
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