We have used a novel modeling technique, based on combining information from several preexisting structures, to generate a three-dimensional (3D) model for the RNA stem-loop responsible for translational repression of the MS2 RNA bacteriophage replicase. Specific features of the model have been tested experimentally by chemical and enzymatic structural probes; results from these experiments have been used to "improve" the model by fixing initial assumptions. The new model and chemical modification data are in part consistent, and further predictions are being tested. The modeling algorithm has a wide range of potential applications, particularly to loop regions in proteins and nucleic acids.
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http://dx.doi.org/10.1016/0263-7855(89)80001-3 | DOI Listing |
Sci Rep
January 2025
International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China.
To meet the requirements of the biopharmaceutical industry, improving the yield of recombination therapeutic protein (RTP) from Chinese hamster ovary (CHO) cells is necessary. The human cytomegalovirus (CMV) promoter is widely used for RTP expression in CHO cells. To further improve RTP production, we truncated the human CMV intron and further evaluated the effect of four synthetic introns, including ctEF-1α first, EF-1α first, chimeric, and β-globin introns combined with the CMV promoter on recombinant expression levels in transient and stably recombinant CHO cells.
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January 2025
MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
Bulk ATAC-seq assays have been used to map and profile the chromatin accessibility of regulatory elements such as enhancers, promoters, and insulators. This has provided great insight into the regulation of gene expression in many cell types in a variety of organisms. To date, ATAC-seq has most often been used to provide an average evaluation of chromatin accessibility in populations of cells.
View Article and Find Full Text PDFCommun Biol
January 2025
Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA.
In mammalian oocytes, large-scale chromatin organization regulates transcription, nuclear architecture, and maintenance of chromosome stability in preparation for meiosis onset. Pre-ovulatory oocytes with distinct chromatin configurations exhibit profound differences in metabolic and transcriptional profiles that ultimately determine meiotic competence and developmental potential. Here, we developed a deep learning pipeline for the non-invasive prediction of chromatin structure and developmental potential in live mouse oocytes.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Medical Oncology, Laboratory of Tumor Immunology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
Isocitrate dehydrogenase 1/2 mutant (IDHmt) astrocytoma is considered a T cell-deprived tumor, yet little is known regarding the phenotypes underlying T cell exclusion. Using bulk, single nucleus and spatial RNA and protein profiling, we demonstrate that a distinct spatial organization underlies T cell confinement to the perivascular space (T cell cuff) in IDHmt astrocytoma. T cell cuffs are uniquely characterized by a high abundance of gemistocytic tumor cells (GTC) in the surrounding stroma.
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January 2025
Shaanxi Key Laboratory of Plant Nematology, Bio-Agriculture Institute of Shaanxi, Xi'an, China.
Ditylenchus destructor, commonly known as the potato rot nematode, is a significant plant-parasitic pathogen affecting over 120 plant species globally. Effective control measures for D. destructor are limited, underscoring the need a high-quality reference genome to understand its pathogenic mechanisms.
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