When former PhD students visit your lab

This week my former PhD student Rajendhran Rajakumar was visiting the lab to finish some experiments. He is a Postdoctoral Fellow in Martin Cohn's lab at the University of Florida chasing ancestral genetic potentials in sharks and will soon begin his second Postdoc at Harvard University in Nobert Perimon's lab where he will master the art of the fly before coming back to his beloved ants. 

Rajee Rajakumar in Action at the Entomology Conference 2016

Rajee came back to finish some critical experiments for his next big paper. His enthusiasm and positive attitude renergized the lab, and we ate lots of sharwerma and fish and chips, so come back anytime Rajee!

Here is Rajee, master manipulating the ants:

Lets hope those experiments work! I love when my former students come back and I get the chance to see how they have matured and become independent scientists, it makes me feel very very proud, after all their success is my success ... We need more young and aspiring minds in Science. As for Rajee, I have no doubt he will reach for the stars and make it big, and soon I will be visiting his lab to learn new techniques and he will pay for my shawarma and fish and chips. 

Welcome back Rajee!

Ehab Abouheif

04 May 2017

Ant Arbiters

Follow McGill undergraduates around the ant lab to catch a glimpse of the volunteering experience, project opportunities, and rudiments of colony caretaking. 

Video by Easton Houle with McGill's Media Relations Office.

The latest in gene regulation: a tribute to François Jacob

A conference titled "Genetic Control of Development and Evolution" was held at the Pasteur Institute in Paris in the autumn of 2015. The conference was a tribute to François Jacob for his contribution to the study of gene regulation. With the help of QCBS funding I was able to present my work at this conference.

My poster at the conference was about endosymbiotic bacteria of ants of the genus Camponotus. We show that the symbiont has driven major rearrangements in early egg development in order to ensure stable endosymbiosis and transmission to the next generation. I received excellent feedback at the conference that helped understand the data in a better light.

The conference was a broad update on gene regulation with reference to development and evolution. Since Jacob and Monod a lot has been learnt about gene regulation. Enhancers, the DNA elements that regulate the levels, timing and spatial extent of gene expression was one of the major themes of the conference. Many presenters showed how suboptimal binding sites make optimal enhancers wherein weak binding sites and ‘half’ binding sites play a major role in specificity of gene expression. Michael Levine of University of Berkley, uses artificial enhancers generated by mutating transcription factor binding sites and the spacing between them. He showed that native enhancers are weak in comparison to artificially generated optimized strong enhancers. The native enhancers are more specific, the stronger enhancers show mis-expression. Kenneth Zaret of the University of Pennsylvania showed that the recognition sites of Pioneer Factors (proteins that initiate release of chromatin bound DNA making it active) are half of the recognition sites of other transcription factors. This feature allows them to bind while allowing the other side of DNA to remain bound to histones. This binding is not sufficient and requires cooperativity and recruitment of other factors meaning many of these bindings are abortive, hence improved specificity. Justin Crocker from Howard Hughes Medical Institute - Ashburn, showed that in the shaven baby locus of Drosophila the relative affinity and specificity of binding sites have an inverse relationship implying that high affinity binding sites may actually bind other genes and decrease specificity. When he changes a low affinity site into a high affinity site it results in mis-expression. He also showed that in different species low affinity binding sites are poorly conserved but are functional in their respective contexts. Marion Guéroult-Bellone from CNRS Montpellier showed how in vitro expression assays are different from in vivo data in terms of levels of expression and reiterated a known fact that spacing between binding sites regulates levels of expression. François Spitz of EMBL Heidelberg showed that long distance enhancers act dynamically activating several genes at the same time where an appropriate TATA box is found at specific optimal distances from it. They use a reporter assay with one enhancer and test for all expressed regions of about 200 kbp region in both directions. If the enhancer was flipped, it affected a reporter at a similar distance in the opposite direction and resulted in a pattern mirroring its activity albeit only when appropriate TATA boxes fell in its range of activity. This pattern of activation is consistent with Topologically Associating Domains; meaning in 3D when a piece of DNA falls in the vicinity of another piece of DNA they interact regardless of their base-pair distance. 

Another major theme of the conference was chromatin remodeling for gene regulation.  Edith Heard from Curie Institute in Paris talked about mono-allelic gene expression in mammals. Repression of the X-chromosome copies in females is well-known, she showed that the X-chromosome that gets inactivated is randomly chosen such that two females, even if identical twins, are different. In addition there are two inactivation waves initiated by the Xist locus. The first one initiates early during development and is maintained throughout development, this one is initiated by the paternal locus. The second one is initiated at the blastocyst stage that initially kicks in both alleles and then stabilizes to persist in one allele inactivating it and not does not do so in the other allele that stays active.  This means that females are mosaics due to random X-inactivation. Gerarld Crabtree of Stanford talked about BAF complexes that are polycomb repressor complexes (PRCs), which seem to be opposing both PRC1 and PRC2 regulating both assembly and disassembly of chromatin.  Bluma Lesch of Whitehead Institute Cambridge, USA showed that developmental regulatory genes remain in the poised state in the Germline in which they contain opposing histone states H3K4me3 and H3K27me3 and are transcriptionally repressed. They continue in the poised state in the gamete stage and this phenomenon is conserved from drosophila to mammals.

A couple of interesting talks used transcriptome sequence analysis to establish relatedness of cells or tissues. Jacob Musser of EMBL Heidelberg used this method to test for relatedness between dinosaurs feathers/scales and bird feathers using scales on the feet of chickens. Principle component analysis of transcriptome sequences of chicken feathers, chicken scales (of feet), chicken nails, alligator scales, and alligator nails show relatedness between bird feathers (not scales of feet) with alligator scales. Alexander Van Oudenaarden of Hubrecht Institute, Utrecht has managed to find a way to separate single cells from the bone marrow blood precursors and RNA sequence them one cell at a time to look for shared expressed sequences. He then correlates their spatial proximity or distance with the number of shared genes. This analysis confirms some of known relationships in tissue precursors and points to spatial information in precursor cells of bone marrow, a site for multiple stem cells. Shahragim Tajbakhsh of Pasteur Institute – Paris showed that the shared program for development of the craniofacial muscles and esophagus muscles is not conserved in birds (birds do not need to chew and swallow). But interestingly basal animals (Ciona being one) have this program. He suggested that the birds might have lost it and more interestingly the craniofacial muscle developmental program may actually have been coopted from the esophageal program. 

Patricia Wittkopp of University of Michigan does experimental evolution in Drosophila and yeast from different wild and lab sources. She has developed a system with two different cis-alleles for the same gene, each driving a different FP (red/yellow) in the same organism; meaning the same trans-acting background driving two different cis-alleles. Using this system she shows that there is higher cis-regulatory divergence in an evolving population, implying that cis regulatory divergence may be favored by natural selection. She also uses induced C->T and G->A mutations and compares them with natural occurring polymorphisms, which showed that natural polymorphism form a subset of induced mutations in terms of noise indicating that noise is selected against in natural selection.

Overall great fun and highly inspiring!

Epigenetic and Complex Social Behaviour

Click link below to check out latest discovery from Shelly Berger's lab at the University of Pennsylvania linking epigenetics and complex social behaviour in ants  

Bipolar Drug Turns Foraging Ants to Scouts

An Introduction to the Beautiful Sky Islands of Arizona

 Check out this video to see why the Abouheif Lab collects ants in the Sky Islands of Arizona. In short, Sky Islands are a replicated natural experiment for evodevo studies, a unique opportunity to study predictability of evolution in respond to past, present, and future climate change!

Abouheif Lab celebrates its 50th publication!

After 12 years @ McGill we hit our 50th!

Its hard to describe the feeling really, it seems like one is running on a trend mill publishing one paper after another, until you lift up your head one day, and realize, wow - I hit 50! I realized this as I had to submit an updated version of my CV, and decided to number my publications. That when I realized we hit a milestone for the Abouheif lab ...

Each publication has it unique flavour and challenges though, and they the experience in publishing each one is etched in my head. I occasionally go back and re-read my papers, and like smelling a scent that reminds you of a particular person, event, or place, each paper brings back memories. I remember, for example, laughing uncontrollably with Marcos Nahmad, my first graduate student (now Professor at UNAM in Mexico!), while trying to express a tongue-twisting thought involving multiple feedback loops. I also remember my discussions with my former postdoc Abderrahman Khila (now a CNRRS Group Leader in Lyon France!) trying to gesture how water striders wrap their legs around their bodies at the Castel Cafe on Sherbrooke, only to realize it looked like we were insulting people with our gestures! And there many more stories I could tell. Each paper is truly an an intellectual journey and a personal adventure with my students. I am lucky to be in science and experience these journeys and adventures...

So on the occasion of this 50th publication, I owe a huge debt of gratitude to my Mentors (PhD and Postdoc Advisors) and Students for making it all happen ... Thank you!

And there is no better way to celebrate our 50th publication than with a real bang, it was covered in Science magazine. This paper, all inclusive form start to finish, took us 13 years to publish, so it really is a great milestone in the legacy of the Abouheif Lab ...

The Eco-Evo-Devo of Sky islands: 

A view of one Sky Island by Standing on another

Click here to read Science news article covering our paper

Winged and Wingless Ant Queens of Monomorium emersoni

Click here to listen to podcast in Science about our work!

Former PhD student Marie-Julie Fave collecting 

Monomorium emersoni on the top of a Sky Island

Click here to read our paper in BMC Evolutionary Biology 

Long Island Adventures

By Angelica Lillico-Ouachour
MSc Student, Abouheif Lab

Our trip to Long Island, NY was quite the adventure! Our first stop was the Biology & Genomics of Social Insects Conference at Cold Spring Harbor. We arrived late in the evening and were able to catch Gene Robinson's talk on transcriptional regulation and metabolism in honeybees to kick off the meeting. As a new scientist in this field, this was an amazing experience and really set the tone for the rest of the conference.

After a few beers and a good night's sleep, we were able to listen to more talks throughout the next day and remainder of the conference. These talks were not only academically exciting but they were compellingly delivered. Some highlights for me were: 

• Dr. Laurent Keller, “The influence of genes and environment on behavior and social organization”
• Dr. Christina Grozinger, “Pheromonal mediation of cooperation and conflict in social insects”
• Dr. Deborah Gordon, “Evolution of the regulation of foraging in harvester ants"

Did I mention that Cold Spring Harbor itself was beautiful?!

Stunning!

Travis and Juni admiring the view.

Our next stop in Long Island was Medford and the New York Pine Barrens to collect ants! Long Island is a great place to collect Pheidole morrisi and this time of year proved to be quite fruitful. We found 11 colonies and several had multiple queens! In fact, Juni and Travis broke an Abouheif lab record and found one colony with 7 queens (previous record: 6 queens). The best part of this visit was meeting with Ehab's friend, Ray Sangwald, who is a remarkable citizen scientist. He is incredibly passionate about slave raiding ants and his backyard is full of colonies that he has collected data on for over 60 years! 

We also had a little adventure to collect in the New Jersey Pine Barrens with Kevin Purce, a PhD student in Dr. Sean O'Donnell's lab at Drexel University, and Maria Traficante, a technician in Dr. Danny Reinberg's lab at NYU. They were great field companions and, although we didn't find any Pheidole morrisi, we did find Pheidole pilfera and some rogue golf balls on the ATV course adjacent to the forest.

Travis collecting ants in style.

This week long trip was an incredible learning experience and a fantastic motivator. I feel so lucky that at this stage in my career I was able to both listen to experts in the field and obtain field experience in one go.