bims-cateng 2023-12-10 papers

Issue of 2023‒12‒10
three papers selected by
Chance Bowman, Dartmouth College

Curr Opin Biotechnol. 2023 Dec 04. pii: S0958-1669(23)00136-2. [Epub ahead of print]85 103026

RNA-based controllers for engineering gene and cell therapies.

Engineered RNA-based genetic controllers provide compact, tunable, post-transcriptional gene regulation. As RNA devices are generally small, these devices are portable to DNA and RNA viral vectors. RNA tools have recently expanded to allow reading and editing of endogenous RNAs for profiling and programming of transcriptional states. With their expanded capabilities and highly compact, modular, and programmable nature, RNA-based controllers will support greater safety, efficacy, and performance in gene and cell-based therapies. In this review, we highlight RNA-based controllers and their potential as user-guided and autonomous systems for control of gene and cell-based therapies.

DOI: https://doi.org/10.1016/j.copbio.2023.103026

Nat Methods. 2023 Dec 06.

Embryo mechanics cartography: inference of 3D force atlases from fluorescence microscopy.

Sacha Ichbiah, Fabrice Delbary, Alex McDougall, Rémi Dumollard, Hervé Turlier.

Tissue morphogenesis results from a tight interplay between gene expression, biochemical signaling and mechanics. Although sequencing methods allow the generation of cell-resolved spatiotemporal maps of gene expression, creating similar maps of cell mechanics in three-dimensional (3D) developing tissues has remained a real challenge. Exploiting the foam-like arrangement of cells, we propose a robust end-to-end computational method called 'foambryo' to infer spatiotemporal atlases of cellular forces from fluorescence microscopy images of cell membranes. Our method generates precise 3D meshes of cells' geometry and successively predicts relative cell surface tensions and pressures. We validate it with 3D foam simulations, study its noise sensitivity and prove its biological relevance in mouse, ascidian and worm embryos. 3D force inference allows us to recover mechanical features identified previously, but also predicts new ones, unveiling potential new insights on the spatiotemporal regulation of cell mechanics in developing embryos. Our code is freely available and paves the way for unraveling the unknown mechanochemical feedbacks that control embryo and tissue morphogenesis.

DOI: https://doi.org/10.1038/s41592-023-02084-7

J Biol Phys. 2023 Dec 06.

Microfluidic technology for cell biology-related applications: a review.

Joydeb Mukherjee, Deepa Chaturvedi, Shlok Mishra, Ratnesh Jain, Prajakta Dandekar.

Fluid flow at the microscale level exhibits a unique phenomenon that can be explored to fabricate microfluidic devices integrated with components that can perform various biological functions. In this manuscript, the importance of physics for microscale fluid dynamics using microfluidic devices has been reviewed. Microfluidic devices provide new opportunities with regard to spatial and temporal control over cell growth. Furthermore, the manuscript presents an overview of cellular stimuli observed by combining surfaces that mimic the complex biochemistries and different geometries of the extracellular matrix, with microfluidic channels regulating the transport of fluids, soluble factors, etc. We have also explained the concept of mechanotransduction, which defines the relation between mechanical force and biological response. Furthermore, the manipulation of cellular microenvironments by the use of microfluidic systems has been highlighted as a useful device for basic cell biology research activities. Finally, the article focuses on highly integrated microfluidic platforms that exhibit immense potential for biomedical and pharmaceutical research as robust and portable point-of-care diagnostic devices for the assessment of clinical samples.

Keywords: Cancer cell; Cell biology; Cell sorting; Cell stimulation; Microfluidics

DOI: https://doi.org/10.1007/s10867-023-09646-y