The increasing amount and variety of data in biosciences call for innovative methods of visualization, scientific verification, and pathway analysis. Novel approaches to biological networks and research quality control are important because of their role in development of new products, improvement, and acceleration of existing health policies and research for novel ways of solving scientific challenges. One such approach is sbv IMPROVER. It is a platform that uses crowdsourcing and verification to create biological networks with easy public access. It contains 120 networks built in Biological Expression Language (BEL) to interpret data from PubMed articles with high-quality verification available for free on the CBN database. Computable, human-readable biological networks with a structured syntax are a powerful way of representing biological information generated from high-density data. This article presents sbv IMPROVER, a crowd-verification approach for the visualization and expansion of biological networks.
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http://dx.doi.org/10.1007/978-1-4939-7027-8_2 | DOI Listing |
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January 2025
DWI-Leibniz Institute for Interactive Materials e.V., RWTH Aachen University, Forckenbeckstr. 50, 52074, Aachen, Germany.
Compartmentalization is crucial for control over complex biological cascade reactions. In microgels, the formation of discrete compartments allows for simultaneous uptake and orthogonal release of physicochemically distinct drugs, among others. However, many state-of-the-art approaches yielding compartmentalized microgels require the use of specific, though not always biocompatible, components and temperatures well above the physiological range, which may damage possible biological cargo.
View Article and Find Full Text PDFNano Lett
January 2025
Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea.
Analyzing the cell interface is of paramount importance in understanding how cells interact and communicate with other cells, but an advanced analytical platform that can process complex and networked interactions between cell surface ligands and receptors is lacking. Herein, we developed the cell-interface-deciphering lipid nanotablet (CID-LNT) for multiplexed real-time cell analysis. LNT is a nanoparticle-tethered lipid bilayer chip where freely diffusing plasmonic nanoparticles induce scattering signal changes.
View Article and Find Full Text PDFiScience
January 2025
Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Successful pancreatic ductal adenocarcinoma (PDAC) immunotherapy requires therapeutic combinations that induce quality T cells. Tumor microenvironment (TME) analysis following therapeutic interventions can identify response mechanisms, informing design of effective combinations. We provide a reference single-cell dataset from tumor-infiltrating leukocytes (TILs) from a human neoadjuvant clinical trial comparing the granulocyte-macrophage colony-stimulating factor (GM-CSF)-secreting allogeneic PDAC vaccine GVAX alone, in combination with anti-PD1 or with both anti-PD1 and CD137 agonist.
View Article and Find Full Text PDFiScience
January 2025
College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, Jiangsu Province, P.R. China.
Pyroptosis plays an important role in attracting innate immune cells to eliminate infected niches. Our study focuses on how influenza A virus (IAV) infection triggers pyroptosis in respiratory epithelial cells. Here, we report that IAV infection induces pyroptosis in a human and murine airway epithelial cell line.
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January 2025
State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
Lignin valorization is crucial for achieving economic and sustainable biorefinery processes. However, the enzyme substrate preferences involved in lignin degradation remain poorly understood, and low activity toward specific substrates presents a significant challenge to the efficient utilization of lignin. In this study, we investigated the substrate promiscuity of Ado, a key enzyme involved in lignin valorization.
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