|Associate Professor||Centre for Nano Science and Engineering|
|Varsha Singh||Assistant Professor||Molecular Reproduction, Development and Genetics|
|Vijay Mishra||Staff||Centre for Nano Science and Engineering|
|Navakanta Bhat||Professor||Centre for Nano Science and Engineering|
|Partha Pratim Talukder||Assistant Professor||Computational and Data Sciences|
A Biological Cyber-Physical Systems (bio-CPS) view of human organs offers unprecedented opportunities to bring together disparate topics including engineering-oriented study of biological molecules and cells, clinical findings, diagnostics and therapeutics, engineering interventions, and computational modeling. While medical CPS deals with self-critical, context-aware, networked medical devices, bio-CPS uses biological cells, bacteria, and viruses as the physical entities that are also capable of processing information and interacting in a networked manner, through built-in sensing and actuation. In this project, we focus on the gut, which includes the entire gastrointestinal tract from the mouth to the rectum.
The gut plays a big role in determining the well-being of a complex organism. It comprises a number of cells that perform different functions, ranging from stem cells that continuously regenerate the lining of the gut every four days; gut-hormone producing cells; epithelial cells that line the gut; mucus-producing cells; immune cells, and nerve cells. The Enteric Nervous Systems (ENS) is an important component of the gut. Adding to this complexity is the existence of almost a trillion microorganisms present in the gut, ranging from bacteria to viruses and fungi. This complex organization is now recognized as playing an important role in complex diseases as disparate as diabetes and autism.
This project focuses on diarrheal diseases, which cause nearly 3,00,000 infant and child mortality in India. A team-member (Sandhya S. Vishweswariah) has ongoing projects focusing on a diarrheal disease supported by the Department of Biotechnology, the Bill and Melinda Gates Foundation, and the Norwegean Research Council. So far, animal models have been developed to understand the functioning of the receptor for the bacterial toxin involved in the disease. What has become apparent from these studies is that in vitro models and computational models not only help understand the disease processes and make way for testing new drugs and therapies. There are open questions such as stochasticity in the response of the gut-epithelial cells to bacterial toxins and the effect of peristalsis on the gut-epithelium. These two aspects prompted a bioCPS approach to address two problems, as described next.
The technical following descriptions of the two interrelated problems should be understood in the context of a biological systems modeled in light of a cyber-physical system. In the first, single cell level responses will be gathered from millions of cells using an already available High Content Imaging system in the IISc BioSystems Science and Engineering (BSSE) facility. The resulting big data will be analyzed using machine learning algorithms to identify patterns and causative relationships. Furthermore, data from RNA sequence analysis (RNSseq) will be used to find nodes of regulation, which in turn is fed back to control cellular responses. In the second, gut-cells will be cultured on microfabricated chips as an in vitro model wherein biochemical cell signals and cell-level forces are measured in situ. Here, the role of ENS is partially provided by cell-level external actuation using microfabricated active scaffolds, in response to measured sensory data. Here, biological cells act as agents in the cyber-physical systems.
- Stochastic responses to signaling molecules that result in diarrhea: Elevation of cyclic nucleotides such as cAMP and cGMP elicit a series of complex changes in the gut epithelium that leads to increased fluid and ion secretion from the cell. We propose to develop fluorescence sensors that monitor the levels of cAMP and cGMP in the cell and will study changes in concentrations in cAMP and cGMP in millions of cells, at a single cell level. These changes will be analyzed by acquiring high content imaging approaches with the InCell Analyzer in BSSE (Sandhya S. Visweswariah). The large amount of data will be analyzed to determine whether there are patterns in the way individual cells respond (Ambedkar Dukkipati). If so, groups of cells with distinct responses can be isolated using cell-sorting, and gene expression in these cells can be analyzed using RNAseq. Once again, a large amount of data will be obtained, which needs to be analyzed to determine a systems response by the cell. Identifying nodes of regulation (Nagasuma Chandra) will then allow manipulating gene expression in a feed-back loop to control cellular responses.
- Gut-on-chip in vitro model: We will build a ‘gut-on-chip’ model using microfluidic devices and designer scaffolds with suitable materials (Kaushik Chatterjee and G.K. Ananthasuresh). We will mimic the peristalsis in the gut by an in-built device that can stretch and contract individual or groups of cells. Culturing cells on static supports versus those with continuous mechanical stress should is likely to alter levels of signaling molecules in the cell (Sandhya S. Visweswariah). These will be detected by metabolomic and other biochemical approaches (Sandhya S. Visweswariah) and viewed in a systems context. Depending on the changes seen, we will try to construct synthetic circuits such that these changes can be detected using luminescence approaches. The light emitted can then be detected and fed back to the system to reduce or enhance stretching (Sandhya S. Visweswariah, G.K. Ananthasuresh, Nagasuma Chandra).
The bioCPS approaches we are proposing here, to the best of our knowledge, are not being pursued in the world at this time. The project is truly interdisciplinary and involves the expertise of a biologist, a materials engineer, a mechanical engineer, a computer scientist, and a systems biologist. Addressing questions related to the gut is of contemporary importance as evidenced even in the popular press.