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Summer Internship at Cambridge MRC Stem cell Institute – Part 2

Scientific Work

My time in Srinjan’s lab was really very exciting and fun thanks to amazing lab members like Maike, Igor, Stan, Oliver Aelun and Srinjan himself. The environment of the institute is very relaxed but also very focused which is perfect combination for a research institute.

My lab mainly focuses on chromatin dynamics. I mainly worked to develop an imaging method to visualise the movement of a specific loci (Sox1) of genome in live cells over a period of time. This can be used to obtain movement patterns and study the change in genome organisation, folding and ordering, compaction, mechanistic changes due to various factors or different small molecule drugs as well as during various stages of development.

Single molecule chromatin dynamics in live cells
Source: https://www.stemcells.cam.ac.uk/

Recently, there a method has been developed to do this, however it was inefficient as it could capture short time frames (~30 – 60 sec) and collect only 2D information, which is not adequate to make any of the above mentioned conclusions. I was able to improve DNA live cell imaging at least 10 times that of the current methods (~25 mins) and also enable to collect information in 3D using Double Helix Point Spread Function based imaging (DHPSF), which gives a holistic idea of the gene locus movement.

DHPSF (3D) image data analysis using matlab

We collaborated with a few labs for this project.

Mehdi from Kevin Chalut’s lab was a great guide who taught me all the cell culture experiments. I carried out all the imaging in collaboration with Sir David Klenerman lab in Department of Chemistry under direct supervision of Srinjan. Since, the concepts of imaging are new to me, I had countless doubts and Srinjan was always ready to answer them with patience. It was wonderful to learn something new about the same topic every-time I talked to him!!

While my classmates were learning about Illumina sequencing in the course here at Stockholm, I was working on the instruments in THE lab that invented it. Dave is knighted for the invention of Illumina sequencing which is widely used today in almost all the labs that perform next generation sequencing. It was a very exciting experience to work in the lab and on the instruments where something like Illumina was invented.

Home built modified Light Sheet microscope setup- monitor control (left), stage and incubator(center) and laser alignment and control(right) 

We also collaborated with Brian Hendrich lab from Stem Cell and Ernest Laue lab.

Life in Cambridge

Cambridge is a very beautiful town with lots of things to enjoy. First and foremost are the colleges and their grounds.

Kings college grounds

There are many museums to visit which hold a lot of history. Even the pubs have history.

Eagle Pub – Where Watson and Crick announced the structure of DNA for the first time

Punting is a famous activity. And just simply walking around the town itself is a enjoyable.

Punting!