Research

PBL is broadly interested in the process of biological evolution. 

Currently, I am analysing the microbiomes of Drosophila populations. We use two approaches: 

• To know the microbiome composition, we sequence 16S rRNA genes from the fly microbiome and 

• To understand functional role of the microbiota on the host, we generate axenic (i.e. microbe-free) flies 

We are seeing that the microbiome composition in our lab fly population varies with age, sex, diet, and evolutionary history. We are able to reproduce broad trends seen in fly microbiome literature in terms of how microbes influence host biology. We plan to study contribution of microbiome over longish timescales (over multiple host generations).

We are also working on an individual-based computational model (IBM) that can capture host-microbiome eco-evolutionary dynamics. 

Link: https://sites.google.com/a/acads.iiserpune.ac.in/sdlab/pbl-iiser-p

In eukaryotes, heterochromatin (compact form of DNA) plays a key role in packaging, protecting as well as regulating the expression of genetic material. In S. pombe (fission yeast), the nuclear RNA interference (RNAi) machinery is involved in the formation of heterochromatin, and it appears likely that a similar process may function in mammalian cells. We set out to address the following questions: how does the first wave of the RNAi machinery localize to the repeats, and what role do the DNA or RNA sequences play in this process?

To understand the role of DNA/RNA elements in "attracting" RNAi machinery to certain genetic loci, we were developing a modified two-hybrid assay in the fission yeast. In this assay, a battery of candidate ncRNA elements will be tethered to the ura4 locus (active gene) in the yeast genome, and the ability of the tethered elements to silence the locus will be assessed using 5-FOA assay.

Link: https://asevilimedulab.wordpress.com/

The lab uses mathematical modelling tools from systems biology and control theory to aid in the study and manipulation of biological systems.

The publication abstract summarising my work with Brian:

Quantitative characterizations of horizontal gene transfer are needed to accurately describe gene transfer processes in natural and engineered systems. A number of approaches to the quantitative description of plasmid conjugation have appeared in the literature. In this study, we seek to extend that work, motivated by the question of whether a mathematical model can accurately predict growth and conjugation dynamics in a batch process. We used flow cytometry to make time-point observations of a filter-associated mating between two E. coli strains, and fit ordinary differential equation models to the data. A model comparison analysis identified the model formulation that is best supported by the data. Identifiability analysis revealed that the parameters were estimated with acceptable accuracy. The predictive power of the model was assessed by comparison with test data that demanded extrapolation from the training experiments. This study represents the first attempt to assess the quality of model predictions for plasmid conjugation. Our successful application of this approach lays a foundation for predictive modelling that can be used both in the study of natural plasmid transmission and in model-based design of engineering approaches that employ conjugation, such as plasmid-mediated bioaugmentation.

Link: https://math.uwaterloo.ca/~bingalls/

The publication abstract summarising our work :

To study chromatin transitions in a paradigm of differentiation associated gene expression (from vegetative cells to gametes to zygotes), we devised a systematic methodology to obtain MNase digested nucleosomal ladders from cell wall containing wild type strains of Chlamydomonas reinhardtii . Using glass or zirconia beads to abrade the cell wall by controlled vortex and incubation conditions, we successfully permeabilized whole cells to introduce MNase into the nucleus, in situ. This abrasion based introduction of extraneous enzymes proved efficacious not only in multiple cell types, but in other unicellular species as well (Scenedesmus and Saccharomyces), widening the applicability of the quick methodology to molecular probing of epigenetic states in multiple species, without having to extract nuclei. Considering its simplicity, the method also harbours potential to be adapted for DNase I or ATAC-seq mapping of chromatin structure, even in Chlamydomonas as an epigenetic model.

Link: https://www.researchgate.net/lab/Subhojit-Sen-Laboratory-of-Epigenetics-Subhojit-Sen