Diffusion and migration play pivotal roles in microbial communities - shaping, for example, colonization in new environments and the maintenance of spatial structures of biodiversity. While previous research has extensively studied free diffusion, such as range expansion, there remains a gap in understanding the effects of biologically or physically deleterious confined environments. In this study, we examine the interplay between migration and spatial drug heterogeneity within an experimental meta-community of . , a Gram-positive opportunistic pathogen. When the community is confined to spatially-extended habitats ('islands') bordered by deleterious conditions, we find that the population level response depends on the trade-off between the growth rate within the island and the rate of transfer into regions with harsher conditions, a phenomenon we explore by modulating antibiotic concentration within the island. In heterogeneous islands, composed of spatially patterned patches that support varying levels of growth, the population's fate depends critically on the specific spatial arrangement of these patches - the same spatially averaged growth rate leads to diverging responses. These results are qualitatively captured by simple simulations, and analytical expressions which we derive using first-order perturbation approximations to reaction-diffusion models with explicit spatial dependence. Among all possible spatial arrangements, our theoretical and experimental findings reveal that the arrangement with the highest growth rates at the center most effectively mitigates population decline, while the arrangement with the lowest growth rates at the center is the least effective. Extending this approach to more complex experimental communities with varied spatial structures, such as a ring-structured community, further validates the impact of spatial drug arrangement. Our findings suggest new approaches to interpreting diverging clinical outcomes when applying identical drug doses and inform the possible optimization of spatially-explicit dosing strategies.
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http://dx.doi.org/10.1101/2024.11.21.624783 | DOI Listing |
Nat Commun
December 2024
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Hodgkin Reed-Sternberg (HRS) cells of classic Hodgkin lymphoma (cHL), like many solid tumors, elicit ineffective immune responses. However, patients with cHL are highly responsive to PD-1 blockade, which largely depends on HRS cell-specific retention of MHC class II and implicates CD4 T cells and additional MHC class I-independent immune effectors. Here, we utilize single-cell RNA sequencing and spatial analysis to define shared circulating and microenvironmental features of the immune response to PD-1 blockade in cHL.
View Article and Find Full Text PDFComput Struct Biotechnol J
December 2024
College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China.
Accurate prediction of drug-target binding affinity remains a fundamental challenge in contemporary drug discovery. Despite significant advances in computational methods for protein-ligand binding affinity prediction, current approaches still face substantial limitations in prediction accuracy. Moreover, the prevalent methodologies often overlook critical three-dimensional (3D) structural information, thereby constraining their practical utility in computer-aided drug design (CADD).
View Article and Find Full Text PDFJ Transl Med
December 2024
Department of Urology, Xinjiang Medical University Affiliated Cancer Hospital, Urumqi, China.
Background: Immune checkpoint inhibitors (ICIs) are a cornerstone therapy for advanced renal cell carcinoma (RCC). However, significant rates of primary resistance hinder their efficacy, and the underlying mechanisms remain poorly understood. This study aims to unravel the tumor-immune interactions and signaling pathways driving primary resistance to ICIs in RCC.
View Article and Find Full Text PDFDrug Discov Today
December 2024
State Key Laboratory of Green Pesticide, Central China Normal University, Wuhan, 430079, China.
Drug discovery is essential in human diseases but faces challenges because of the vast chemical space. Molecular generation models have become powerful tools to accelerate drug design by efficiently exploring chemical space. 3D molecular generation has gained popularity for explicitly incorporating spatial structural information to generate rational molecules.
View Article and Find Full Text PDFInt J Pharm
December 2024
SkinAxis LLC, Cedar Knolls, NJ, USA. Electronic address:
In this study we evaluated the effects of flow lamination on aerosol flow dynamics and deposition at the exit point in testing models with spatial barriers (narrowing or curving).We compared ModiFlow (MF) to an idealized Standard Spacer (SS) in their efficiency of delivery of aerosolized medication (fluticasone) across different types of spatial barriers. Fluticasone propionate HFA Inhaler from Prasco Labs 220 µg per actuation was used to deliver 1 spray in each test tube.
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