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Current and Future Role of Circulating DNA in the Diagnosis and Management of Urothelial Carcinoma.
Am Soc Clin Oncol Educ Book
January 2025
Division of Oncology, Department of Medicine, University of Washington, Seattle, WA.
The growing sophistication of tumor molecular profiling has helped to slowly transition oncologic care toward a more personalized approach in different tumor types, including in bladder cancer. The National Comprehensive Cancer Network recommends that all patients with stage IVA and stage IVB urothelial carcinoma have molecular analysis that integrates at least testing to help facilitate the selection of future therapeutic options. Sequencing of tumor-derived tissue is the mainstay to obtain this genomic testing, but as in other cancers, there has been extensive research into the integration of liquid biopsies in longitudinal management.
View Article and Find Full Text PDFMultiplex generation and single-cell analysis of structural variants in mammalian genomes.
Science
January 2025
Department of Genome Sciences, University of Washington, Seattle, WA, USA.
Studying the functional consequences of structural variants (SVs) in mammalian genomes is challenging because (i) SVs arise much less commonly than single-nucleotide variants or small indels and (ii) methods to generate, map, and characterize SVs in model systems are underdeveloped. To address these challenges, we developed Genome-Shuffle-seq, a method that enables the multiplex generation and mapping of thousands of SVs (deletions, inversions, translocations, and extrachromosomal circles) throughout mammalian genomes. We also demonstrate the co-capture of SV identity with single-cell transcriptomes, facilitating the measurement of SV impact on gene expression.
View Article and Find Full Text PDFAccurate Physics-Based Prediction of Binding Affinities of RNA- and DNA-Targeting Ligands.
J Chem Inf Model
January 2025
Schrödinger Incorporated, Cambridge, Massachusetts 02142, United States.
Article Synopsis
- Predicting how well ligands bind to nucleic acids is challenging, which limits the development of small-molecule drugs for diseases like cancer and infections.
- Recent advancements in computational methods, particularly free-energy perturbation (FEP), have improved predictions for protein-ligand binding affinities, but its effectiveness for nucleic acids was unclear.
- This study found that using FEP+ software with the OPLS4 force field can accurately predict binding energies for over 100 ligands interacting with DNA/RNA, achieving predictions that closely match experimental data and could aid drug discovery.
Technologies for studying phase-separated biomolecular condensates.
Adv Biotechnol (Singap)
March 2024
Guangdong Provincial Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, GuangZhou, GuangDong, China.
Biomolecular condensates, also referred to as membrane-less organelles, function as fundamental organizational units within cells. These structures primarily form through liquid-liquid phase separation, a process in which proteins and nucleic acids segregate from the surrounding milieu to assemble into micron-scale structures. By concentrating functionally related proteins and nucleic acids, these biomolecular condensates regulate a myriad of essential cellular processes.
View Article and Find Full Text PDFMetabolic engineering for single-cell protein production from renewable feedstocks and its applications.
Adv Biotechnol (Singap)
September 2024
School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China.
Proteins are indispensable for maintaining a healthy diet and performing crucial functions in a multitude of physiological processes. The growth of the global population and the emergence of environmental concerns have significantly increased the demand for protein-rich foods such as meat and dairy products, exerting considerable pressure on global food supplies. Single-cell proteins (SCP) have emerged as a promising alternative source, characterized by their high protein content and essential amino acids, lipids, carbohydrates, nucleic acids, inorganic salts, vitamins, and trace elements.
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