Thoughts on lab rotations

The thing with first-year rotations in a Ph.D. program is that anxiety starts kicking in somewhere along the way when you consciously identify the lab that you want to join and want to get started right away. Having realized that this is going to be a long journey and rushing into things may not help, I am now gaining patience and perspective, and hope to make the most of the remaining time of my first year.

Rotations are a great way to learn about a lab and get involved in the nitty-gritty of research. I was warned at the beginning by a few seniors that I would either love a lab or reject it within the first few weeks of the rotation. Mind you – this has nothing to do with the science pursued in the lab (one wouldn’t decide to rotate in a lab if they didn’t find the research interesting in the first place). This is more about getting comfortable with the way a lab functions and deciding if the environment is a good fit for you. An eight-week lab rotation is really like an eight-week long interview with a potential PI and the lab! It is essential to identify the kind of relationship you foresee having with your advisor for the next couple of years (and beyond). This is perhaps one of the most important aspects of a rotation for me, next to the research work. A good mentor-mentee relationship can go a long way and can be extremely beneficial to one’s academic/professional career. I prefer having an open channel of communication with my mentor and learn as much as possible from him/her.

Not all graduate programs require laboratory rotations. Many departments or programs accept or reject students simply based on their application and/or an interview. In the UK for example, students are recruited to work on specific projects and grants as a part of their Ph.D. for the time period of around 3 years. This may not benefit the candidates who wish to propose their own ideas and develop their own thesis based on their individual research interests. In the US, for most graduate programs in the life sciences (mainly biology and chemistry), the average time for graduation is around 5-6 years. I believe that the freedom and independence of this system trump the short graduation time of the other systems. Although I am certain that both sides have their set of merits and demerits, at the end of the day, the journey is unique to each one of us and what we make of the experience matters the most.


Blots, cultures and assays concludes rotation two

This week officially concludes my second laboratory rotation in the neuropharmacology lab with research focussed on  G protein-coupled receptors and their application in several neurological disorders such as depression and anxiety. In the eight week duration of my rotation, a few things were achieved with respect to validating the activity of the newly developed M4R-DREADD (a designer M4 muscarinic receptor exclusively activated by a designer drug). Designer receptors are engineered such that they are solely activated by a synthetic ligand. This opens new avenues in the activation and control of G protein-coupled receptors’ function in vivo.

After a long break from my Master’s research, I got back to maintaining two cell lines – CHO (Chinese Hamster Ovary) and HEK293 (Human Embryonic Kidney) cells, in which the opioid receptors were expressed for all my experiments. These cells were used to characterize the receptor signaling by western blot analysis of the downstream MAPK/ERK signaling  upon stimulation by a few agonists/drugs of interest. Luckily, the lab acquired a new fluorescence microscope during this period which helped us observe the recruitment of the β-arretin2 protein by δ-opioid receptors in HEK293 cells stimulated with clozapine-n-oxide, a synthetic ligand.

mrrd-gfp barrest-cherr cno 0 min 20x_Overlay copy
HEK293 with M4R-dreadd 20x
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HEK293 with M4R-dreadd 20x

This week, I had a lot of difficulty in handling the mice. Being my first experience with animal work, watching the mice anxious and struggle while we held them down was hard. I am still pretty unsure about how I feel about animal work (if I HAVE to do it to save my research in the future, I will) but I definitely need more exposure and practice with them.

Overall, this lab taught me a lot, even if some days were stressful and  tiring. I feel like I learned and enhanced many skills in the process (primer design, restriction analysis, cell culture, cloning, western blot, cAMP assay), and got a feel for the lab at the same time. Through the course of these past two rotations, I have met some really smart and dedicated people. In the end, I am grateful to have had this opportunity.

Maintaining laboratory notebooks

One of the first things that I had to do when I started my research in the lab was to create a lab notebook. What started off as a well-groomed, precise and perfectly organised record of my research procedures is now turning into a sloppy mess. Making daily entries of my work has become tiresome and I am slowly losing track of the orderliness while trying to keep up. But guess what? The *perfect* lab notebook simply does not exist.

Page from one of my first lab notebooks.
Page from one of my first lab notebooks.

Lab notebooks are supposed to be a documentation of our research. And no research is perfect. Numerous changes to protocols, adjustments in data and new developments in our exploration as we maneuver through the endless facts and figures are all an integral part of scientific research. A lab notebook which demonstrates all this translucently is ‘almost’ perfect. The essentials like dates, page numbers, goals, protocols, observations, calculations and the results are absolutely fundamental. However, so are the tiny side notes to show changes, end pointers to highlight significant steps, indicators to expose errors & oversights, etc. Further more, pictures of gels, protein expression, spectrophotometer results, blots, gene maps, overview diagrams, illustrations, and experimental designs add unique individual characteristics to each lab notebook.

The intention should be to establish a good record keeping practice, without missing out on any vital details that can be easily understood by all. One of the critical components that I found missing in many books was the answer to the question “why” at the beginning of every protocol/day. I consider this element to be important because many times, we find ourselves lose track of the purpose of a particular procedure or fail to see the larger picture while blatantly repeating steps for the zillionth time.

Another format that one can consider these days are ELNs or electronic lab notebooks. These could be great in terms of simplicity, effortlessness and all the features that accompany it. Images in-between protocols, adding graphs & tables, attaching external files, hyperlinks, organising experiments in different files, creating tabs for managing inventories, etc can all be incorporated into one project file. It is like maintaing an entire lab digitally on a personal computer! Hard copies of the documents can be printed out regularly to serve as an alternate backup. The efficiency of ELNs seems to be drawing a lot of attention from some of the new age scientists.

While this seems to be a new avenue to explore, I am going to give myself enough time and experience to outgrow the good old hardbound notebooks that are going to serve as my memory aid in the future.

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