Adaptation Lab

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

Goodbye Imroze!

We said a fond farewell to Imroze Khan, the first postdoc from the lab. Over the last 4 years or so, Imroze initiated and led work on the ecology and evolution of insect immune function. He is now an Assistant Professor at Ashoka University, where he will continue to work with insect life history and immune function.

New paper: A link between early inflammation, immune function and ageing

All organisms age. One prominent hypothesis suggests that infections experienced early in life accelerate ageing. In collaboration with Jens Rolff, Imroze tested this idea in mealworm beetles (Tenebrio molitor). He found that young beetles injected with bacterial cell components mounted an immune response that damaged their vital organs – Malpighian tubules, equivalent to kidneys – and resulted in faster ageing. Experimental down-regulation of phenoloxidase (a key component of the immune response) via RNAi allowed beetles to live longer. Similarly, older beetles infected with a live pathogen also lived longer if their immune response was suppressed. Thus, inflammation induced by immune responses may generally accelerate ageing in various contexts. These results suggest that natural selection is nearly blind to immune self-harm because its effects are felt later in life, after peak reproduction. Similar mechanisms may operate in other organisms, as ageing is a feature of most multi-cellular organisms including humans.

Read the early online version of the paper here.

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.