As a young scientist, a “Principal Investigator”, I attended an international conference in Singapore with the calculated intention of presenting some surprising results we had stumbled upon. We had carried out an immunoprecipitation -a technique, where antibodies attached to beads are used to pull down complexes of proteins. In our case, we had pulled down a histone variant, H2A.Z, and by sequencing the associated DNA we could see the genomic locations where these H2A-like-protein binds. We were on to something important, if only I could be sure it was not a technical artifact. We had segregated promoters with high, medium and low expression and found an unexpected correlation between the location of binding and expression. The farther, the binding site of H2A.Z from the transcription start site, the lower the expression of the promoter. This data was of interest to the community because it was the first in vivo nucleosome positioning data from mammalian tissues or organs. I nervously gave the talk, the first talk of the day, to the scattered audience which to my dismay was mostly busy flipping through their abstract books or finishing their coffee. After my talk, one of the people who came and spoke about the work at length was Stephen Turner, the Chief Technical Officer of Pacbio. For those of you, especially students, who are not familiar with Stephen Turner, do check out Turner’s stellar career. Having completed his PhD from Cornell in 2000 studying nano fabricated structures, he founded Pacbio around 2004. I was in awe of this brilliant techno-wizard but I was not exactly a potential customer because I needed shorter reads for higher resolution and Pacbio was uniquely suited for long reads at the time. But to my surprise and relief, he talked only of my research and surprising findings, and while walking away made a statement that was not really clear to me at that time. He said, “There is a tiger in the bushes alright, and you have caught a tail too. But is it the tiger’s tail?”. After I got over the general nerves that go with giving a talk and speaking to a stranger, that too, The Steven Turner, on the flight back, half dozing – I got what he meant. I knew that H2A.Z, sits at certain preferred locations but I had not yet shown that it causes gene activation and how the distance from the Transcription Start Site matters. This remains an open end in my work, but this analogy serves me to think about projects and experiments to this day.
Our research interests often start with the vague citing of some stripes in the bushes. We are not quite sure if they are there or not. How do we find if it is a tiger or a hyena? As a student or postdoc, you are likely to be inducted into a project at this stage. Much like, in the jungle, one may call out to a few others to circle the bush. The next stages aim to make the stripes more visible: get some drums and beaters, if resources permit, a drone fitted with a camera and beat around the bush. In our ncRNA centric lab, these experiments are the over expression, localization and knockdown experiments to see what the situation around the question we are addressing is. In the bushes, the drumbeats and general commotion brings out a little furry creature. A few members, with excited shouts, run after it only to find that it is an inconsequential rodent. In a PhD too, it is not uncommon to get excited about results that turn out to be a temporary distraction. Back to the main bushes; a long tail comes out. The brave ones in the group snare the tail and pull it out. The project moves faster and faster and often the leader lines up the master shooter in the team- gun cocked, on-the-ready, outside the bushes. In the lab, a postdoc with long years of experience and wizard-like technical skills, steps in to close the story. When the striped animal leaps out from the bushes, this skilled hunter gets a single shot, aimed to catch and incapacitate, perhaps not to kill? In the lab, these nail-in-the-coffin experiments need the best reagents- iPSC lines, transgenic models and smoothly working machines, in the hands of the most skilled members. The experiments often need collaborations between temperamentally disparate parties.
The animal is finally caught, and the hunting party is ready to walk back to the village. Of course, there will be reviewers and critics waiting to measure, assess and compare. The old expert hunters will gather around to opine knowledgeably. There will also be little children, excited to watch and tag along in the procession of hunters who went on the tiger hunt, coming home with the kill. This walk fuels their dream of becoming master hunters in their own time. Sometimes the stripes turn out to be dappled sunlight on the coat of a deer that was hiding in the bushes. But what about the long tail, you ask? Maybe the tiger got away! There was a tiger in the bushes and I had a tail in my hand, but was it that tiger’s tail?
The team disbands, the kids go home. Old hunters who had come to assess and comment, go away too. But a few members of the hunting party cannot sleep that night, tossing and turning in bed, waiting for daybreak. They know that another day, they will go back to the jungle. For them it is not a failure, but a pause, before they go on that hunt again, because there certainly was a tiger in the bushes. There certainly was a protein sitting at those promoters.
Not every hunt is put together in pursuit of elusive stripes in the bushes. There are big elephants in the plains, the target is there, visible to everyone. There are hunting parties that ignore the stripes in the bushes, because they are in the game for the big kill. And yet others, who have the patience to lie long hours in wait, alone, with a bait in hand. And yet others, who lay a trap for the little furry creature and get surprised to find the tiger in the trap. But summer training sessions and dissertations are often about walking with the hunting party and picking up their skills and their ways. A Ph.D is at times about small forays after distracting furry creatures, and lying in wait for the big game at other times, sharpening the arrows or building that drone. At the end of a PhD, most of us intuitively know if we would like to keep making the drones, or go hunting with the big teams, or go after that bird in the trees that was, oh, so beautiful, so elusive. A fulfilling day in a group leader’s life is when the tiger is snared, but before that there are many sleepless nights wondering if those stripes in the bushes were real, many days of begging the drummers to join the hunting party, and even some days of telling the kids the stories of the jungle.
Cover picture Credit: Srashti Jyoti Agrawal
Beena Pillai received her early scientific training as a microbiologist and now studies gene regulation in the neural system using diverse models- zebrafish, earthworm, mice and cultured cells to understand the molecular mechanisms underlying neurogenesis, neural cell differentiation and neurodegeneration.