Emergent Biological Systems (Dr. Siddharth Deshpande)

The philosophy of EmBioSys lab

Living systems are an ensemble of countless emerging properties, manifested at cellular, organismal, and population level. It is the self-assembly and self-organization of biomolecules – from amphiphilic lipids forming cell membranes to complementary DNA strands joining together to form an obviously useful genetic code – into a highly functional and complex system that make cells spring to life. Understanding these phenomena is what makes biological soft matter exciting to us. Since cells are so complex, we have a strong liking for bottom-up biology, i.e., studying purified cellular components in a controlled manner. Such minimalistic approach helps to pinpoint cause-effect relationships, but also to design bio-inspired, minimal functional modules – and take a step closer towards synthetic cells!

Current research

We are an international team of enthusiastic scientists with diverse backgrounds. We do interdisciplinary research combining biology with chemistry and physics, while extensively using on-chip microfluidic technology. Following are our key research areas:

Understanding cellular morphogenesis in 3D environments

Amongst a rich diversity of emergent properties cells exhibit, we are currently focussing on the ability of cells to change shape and move, in response to intracellular and extracellular stimuli. Eukaryotic cells do so using a dynamic intracellular protein machinery known as the cytoskeleton, and we are particularly interested in the polymorphic actin filaments. Using purified protein components and OLA, an on-chip liposome production technique that we have developed, we wish to understand, for example, blebbing motility exhibited by cells in 3D environments.

Key publication

Impact of intracellular organization on cytoskeletal dynamics

Impact of intracellular organization on cytoskeletal dynamics
Intracellular compartmentalization is an essential feature of eukaryotic cells, in order to perform and regulate biological functions. Even so, their impact on actin dynamics is highly unexplored, especially using minimal in vitro systems. Two prominent examples are the stiff, bulky nucleus and the numerous membraneless organelles (biomolecular condensates) found inside cells. We wish to study the impact of these compartments in actin-based morphogenesis using suitable microfluidic systems such as condensate-in-liposome structures that we recently developed.

Key publication

Developing microfluidic technologies

As an experimentalist, one wants maximum control over your system, in order to systematically and reproducibly tackle the problem. Microfluidic is a versatile technology that offers such a well-defined and controllable environment. Over the years, we have developed numerous microfluidic assays to tackle important biological questions: Quasi-2D microchambers to study biochemical reactions, flow-assays to understand the surface-sensing mechanism in bacteria, bubble-blowing machines to make cell-mimicking vesicles, etc. We extensively utilize these on-chip tools as well as design new ones.

Key publications

Offered MSc and BSc projects