Biology subjects

Bhattacharjee, T.

Publications and source records attributed to Bhattacharjee, T..

3 recordsLinked to original sources

bioRxiv2023

Jammed microgel growth medium prepared by flash-solidification of agarose for 3D cell culture and 3D bioprinting

1. Introduction ABSTRACT 1. Introduction 2. Materials and methods 3. Results and discussion 4. Conclusion Author contributions Supplementary Information References Cells grown as monolayers on conventional two-dimensional (2D) culture plates are significantly different from their in vivo counterparts in many different ways [1]. In standard flat plate cultures, not only do they exhibit altered morphologies and dynamics [2-4], their gene expression and signal transduction profiles are dramatically altered [5]. Furthermore, cells in vivo are exposed to more complex mechanical cues and chemical fields due to their three-dimensional (3D) packing and access to systemic circulation [ ...

bioengineering↗

bioRxiv2022

Roughening instability of growing 3D bacterial colonies

How do growing bacterial colonies get their shapes? While colony morphogenesis is well-studied in 2D, many bacteria grow as large colonies in 3D environments, such as gels and tissues in the body, or soils, sediments, and subsurface porous media. Here, we describe a morphological instability exhibited by large colonies of bacteria growing in 3D. Using experiments in transparent 3D granular hydrogel matrices, we show that dense colonies of four different species of bacteria--Escherichia coli, Vibrio cholerae, Pseudomonas aeruginosa, and Komagataeibacter sucrofermentans--generically roughen as they consume nutrients and grow beyond a critical size, eventually adopting a characteristic branched, broccoli-like, self-affine morphology independent of variations in the cell type and environmental conditions. This behavior reflects a key difference between 2D and 3D colonies: while a 2D colony may access the nutrients needed for growth from the third dimension, a 3D colony inevitably becomes nutrient-limited in its interior, driving a transition to rough growth at its surface. We elucidate the onset of roughening using linear stability analysis and numerical simulations of a continuum model that treats the colony as an active fluid whose dynamics are driven by nutrient-dependent cellular growth. We find that when all dimensions of the growing colony substantially exceed the nutrient penetration length, nutrient-limited growth drives a 3D morphological instability that recapitulates essential features of the experimental observations. Our work thus provides a framework to predict and control the organization of growing colonies--as well as other forms of growing active matter, such as tumors and engineered living materials--in 3D environments.

biophysics↗

bioRxiv2020

Chemotactic Migration of Bacteria in Porous Media

Chemotactic migration of bacteria--their ability to direct multicellular motion along chemical gradients--is central to processes in agriculture, the environment, and medicine. However, studies are typically performed in homogeneous media, despite the fact that many bacteria inhabit heterogeneous porous media such as soils, sediments, and biological gels. Here, we directly visualize the migration of Escherichia coli populations in 3D porous media. We find that pore-scale confinement is a strong regulator of chemotactic migration. Strikingly, cells use a different primary mechanism to direct their motion in confinement than in bulk liquid. Further, confinement markedly alters the dynamics and morphology of the migrating population--features that can be described by a continuum model, but only when standard motility parameters are substantially altered from their bulk liquid values. Our work thus provides a framework to predict and control the migration of bacteria, and active matter in general, in heterogeneous environments. Statement of SignificanceTypical studies of bacterial motility focus on cells in homogeneous media; however, many bacteria inhabit tight porous media such as soils, sediments, and biological gels. This paper demonstrates how confinement in a porous medium fundamentally alters the chemotactic migration of Escherichia coli. We find that cells use a different primary mechanism to direct their motion in confinement than in bulk liquid. Further, confinement markedly alters the overall dynamics and morphology of a migrating population--features that can be described by a continuum model, but only when standard motility parameters are substantially altered from their bulk liquid values. This work thus provides a framework to predict and control the migration of bacteria, and active matter in general, in heterogeneous porous environments.

biophysics↗