Adaptation Lab

Welcome to Deepa Agashe’s lab at the National Centre for Biological Sciences (NCBS), Bangalore!


NCBS Science Day

Our campus recently hosted an open Science day, when hundreds of school students visited the campus and explored exhibits set up by students and postdocs from many labs. All accounts suggest this was a lot of fun for everyone. Here is an article describing the events.

Here are some pictures of our lab’s tables showcasing different rice varieties, bacteria associated with various plants, animals and inanimate objects, an activity highlighting the role of chance in evolution, and our favourite beetles. Thanks to Laasya, Aparna, Pratibha, Aditi, Anurag, and Parth for making all this interesting!

New paper: Immune priming responses vary across beetle populations

Traditionally, immune memory was thought to be restricted to vertebrates; such adaptive immunity is the reason why early vaccination protects us from later infection. However, a large body of recent work suggests that many insects also show a form of immune memory, whereby exposure to a low dose of a pathogen improves an individual’s response to a subsequent infection with the same pathogen. Although we do not understand the physiological and molecular mechanisms responsible for such immune “priming”, the response may be costly and is often specific to the pathogen (even the strain), suggesting that priming may be an adaptive trait. If so, the strength of the priming response should vary depending on, e.g., selection imposed by local pathogens and the specific costs of mounting the priming response. However, no one had quantified variation in the priming response. We tackled this problem in our latest paper in Ecology and Evolution.

Imroze and Arun did an enormous study to measure the immune priming response of 10 different wild-collected populations of flour beetles as a function of sex and life stage of priming. As predicted, they found substantial variation in the priming response across populations. Interestingly, they also found that ontogenic priming (when larvae are primed, and then infected as adults) conferred the largest survival benefits compared to within-stage or trans-generation priming. These are exciting results because they show that priming is not a ubiquitous response, and set up clear predictions about the relative benefits and costs of priming as a function of stage and sex. The results are also consistent with (though they do not directly support) the hypothesis that priming should evolve under local, specific and strong pathogen pressure. We are now moving ahead with efforts to determine factors responsible for the observed variability in the priming response. Watch this space for more!

Poster awards for Kruttika and Laasya

Our campus recently hosted a conference on Conflict and Cooperation in Cellular Populations (CCCP), featuring a wonderfully diverse set of talks and participants alike. Kruttika presented a poster summarizing her results on the bacterial communities of butterflies, and Laasya put up a last-minute poster on the benefits of altered initiator tRNA content in E. coli. We’re very happy that both of them won prizes for their posters! Congratulations!

Symposium on the Genetics of Adaptation

GeneticsOfAdaptation_posterI am pleased to announce a symposium on the genetic bases of adaptation and evolution, co-organized with my colleagues Gaiti Hasan and Krushnamegh Kunte. The meeting (28 Nov – 2 Dec at NCBS) will bring together evolutionary and development biologists, geneticists and theoreticians. Together, we will aim to synthesize current understanding of and future goals for determining the genetic bases of adaptation and evolution. This is an exciting time for such a synthesis!

We have a terrific lineup of speakers, and we hope to have equally amazing contributed talks and posters from advanced PhD students, postdocs, and young faculty. Applications for oral and poster presentations are due by 15 Sep 2016. More information

New paper: Testing for selection on Shine-Dalgarno-like motifs in prokaryotes

Gaurav’s analysis of the occurrence of Shine-Dalgarno-like motifs in prokaryotic coding regions has just been published in GBE. This is the first bioinformatics analysis we’ve done, and we are pretty pleased with the paper!

Bioinformatics analyses of bacterial genomes have uncovered interesting patterns of specific sequence features. Although it is tempting to invoke selection, it is important to distinguish the effects of selection from genetic drift, biophysical constraints, or indirect selection. For instance bacterial translation initiation usually requires ribosomal binding to the Shine-Dalgarno (SD) sequence in a gene’s 5′ untranslated region. Previous analyses showed that SD-like motifs are rare within protein coding genes of Escherichia coli and Bacillus subtilis (Li et al 2012, Nature). These authors suggested that because ribosomes pause at internal SD-like motifs, selection against them also explains codon bias across bacteria. However, it is important to consider alternative hypotheses. The SD sequence is GC-rich and well conserved across bacteria; hence its occurrence will vary simply as a function of genomic GC% (which ranges from 13-75% across bacteria). Experimental evidence also suggests positive selection on SD-like motifs: “programmed” internal ribosomal pauses are critical for proper folding and targeting of some proteins (e.g. Fluman et al 2014, Elife). We found that after accounting for the genomic GC content, ~50 out of 284 prokaryotic genomes showed no evidence of selection against internal SD-like motifs. Furthermore, selection on these motifs seems to vary according to their location. For instance, the C-terminal ends of genes are relatively enriched in SD-like motifs, potentially to initiate translation of the downstream gene. In contrast, the N-terminal ends of genes are depleted in SD-like motifs, perhaps due to their deleterious effects on local mRNA structure (known to affect gene expression). Our work thus highlights the complicated nature of selection acting on sequence elements and motifs, and the importance of accounting for genome-wide features such as GC content.

News and Plans for summer

We’ve been busy! Here is some good news and fun plans for the summer. Many of us will be zipping across the world to present our work at conferences. If you happen to spot us, do come up to chat!

Gaurav, Vrinda and Saurabh successfully defended their thesis proposals and are now officially stamped and certified PhD students doing important thesis work. Hooray!

Laasya has been nominated for a Young Scientist Medal from the Indian National Science Academy (INSA). Good luck for the final presentation!

Arjit Jere (Garware College, Pune) finished his Master’s thesis working on ant lion pits (I served as Arjit’s thesis guide). Well done, Arjit!

Nilima Walunjkar (IISER Pune) has joined us again, this time for her Master’s thesis project. She will be working on the fitness effects of codon use in Methylobacterium. Welcome!

Aparna and I will be at the Evolution meetings in Austin, USA in June. Aparna will be partly funded by an Infosys Travel Award. Congratulations!

Mrudula and I will be at the SMBE meeting in Gold Coast, Australia in July. This is our first trip to the continent; we can’t wait to see Koalas and Kangaroos!

Gaurav and Laasya will be at an EMBO conference on Ribosome Structure and Function in Strasbourg, France, in July. Gaurav will be partly supported by a travel grant from DBT. Congratulations!

Laasya will also attend the Gordon Conference on Microbial Stress response in South Hadley, USA, in July 2016.

Finally, Gaurav Agavekar (MSc Wildlife student; I am serving as his thesis guide) received an Infosys travel award to attend the 2016 Ant course in Mozambique, Africa, in July. Congratulations!



Our very first insect-gut microbe paper

CoverAshwin’s Master’s thesis work on the gut bacterial communities of dragonflies has been published in Current Science. The paper is highlighted in the “In this issue” section of the journal and supported by a Cover image of a Globe Skimmer (Pantala flavescens) by Shantanu. Good work, both!

In this paper, we describe culturable gut bacterial communities of eight species of dragonflies collected from three different locations in South India. We found that the bacterial communities are largely host-specific, which is a bit surprising since dragonflies are thought to be generalist predators. We also found weaker effects of sampling location and season, suggesting that dragonflies might indeed specialize on different prey leading to variable gut bacterial communities. At the moment these are interesting results that lead us to new hypotheses; we are now testing these ideas with larger datasets and more comprehensive sampling of microbial communities of dragonflies.

You can access the paper here.


New paper: Adaptation via synonymous mutations

Agashe_mbe_coverUpdate: Here is a really nice graphic that Kruttika and Gaurav made, that captures some of the fun results from this work.

Our work showing rapid, parallel adaptation in Methylobacterium extorquens is now out online on the MBE website. The work represents a huge team effort from members of my former postdoctoral lab and my current lab at NCBS- Mrudula, Kruttika, Gaurav and Alefiyah. We are very excited about this paper, partly because of the surprisingly large adaptive benefits of synonymous mutations, and also because we show that no single mechanism underlies these fitness effects. Our understanding of the evolution of codon bias just got murkier, but also that much more interesting- we need new hypotheses!

You can access the paper here, and read a news article about it on the NCBS webpage.

Peering into the dark to shed new light on evolution

Aparna Agarwal, Kruttika Phalnikar and Deepa Agashe

This article originally appeared in the 2016 edition of IMPRINT, the science magazine of the Dept of Zoology, St. Xavier’s College, Mumbai. The issue focused on life in the dark, and we wrote about evolutionary adaptations to darkness. We thought we would share it with others.

Look into the deepest caves

Or remember the darkest hour you’ve seen

Float in the midnight zones of the sea

Or visit the deepest pits your mind has been…

Humans have a strange connection with darkness. Technically, darkness is just the absence of light; yet our language is strewn with examples of how we both fear and are fascinated by the dark at the same time. The parts of the universe that cannot be observed are composed of dark matter. The devil lurks in the dark, while heaven is the light at the end of a tunnel. What we do not understand are the dark arts, while discovering the truth brings facts to light. This obsession with the dark is not unreasonable. As humans – just like many other animals – we rely heavily on our visual system for information about the world we live in. However, many animals have moved away from such a visual bias, and understanding the evolutionary processes that drive this change has enriched our understanding of evolution itself. In the next page or two, we will highlight some of these patterns that dark-adapted organisms have revealed. Continue reading