Tag Archives: summer placement

Shannon Edwards – UCL Genetics Institute

“I am grateful to have gained so much in such a short space of time.”

During my placement at UCL, I was fortunate enough to gain an insight into Computational Biology under the supervision of Jack Humphrey. Having been informed of the functions FUS and TDP-43, I soon learnt that as with many proteins, the change in expression of the genes that code for such RNA- and DNA-binding proteins, respectively, can be argued to characterise many neurodegenerative diseases. In this case, the diseases looked at were ALS and Frontotemporal Dementia. The efficiency with which the analysis of the regulation of genes took place using programming software such as R Studio was apparent from the beginning and this became the main method to manipulate sample data.

Shannon Edwards 1As a practice for writing code, I made use of a publicly available differential expression dataset that compared the gene expression between mice brains that were treated with two antisense oligonucleotides, (ASO’s). One of the ASO’s was a random sequence and the other was specific to the FUS transcript. I found the process for plotting the resultant graphs particularly complex, considering that I am a part of a generation that is said to be ‘tech-savvy’. I believe that practice through an online course teaching coding, as well as creating sample plots whilst at UCL is enough to show the depth of understanding required to make the most out of one week, let alone a PhD or career. Nevertheless, after altering the R script several times I was able to comprehend that the greater the log10 (Base Mean) value, the closer the Log2FoldChange value was to zero, indicating a smaller quantity change, although the areas of clustering can suggest similarities between sub-sections of data. The resulting plot is shown below.

Shannon Edwards 2Arguably the most complicated task was set towards the end of the week. The proposition was that mutations in the TDP-43 gene would impact the RNA-binding ability of the TDP-43 protein, and I used pre-existing data to analyse whether it would act as a knockdown. I found that the hypothesis was difficult to support based on this dataset, and as expected in science; more data would need to be analysed. Using skills within R such as vector arithmetic helped to reach this judgement as it gives rise to additional data such as log10(gene length) which was calculated from given data to produce a plot with fewer points. Also; the ‘for()’ loop function loaded the data into one plot using the same commands, but did so in such a way that each dataset was still uniquely identified with the assistance of different colours, as you can see in the picture above.

My placement allowed me to witness how science calls for patience and the ability to ask the right questions to manipulate and evaluate the data that could add another piece to the puzzle. With thanks to Jack for giving up his time, everyone at UCL for their hospitality (and smoothies) and In2scienceUK for providing me with the placement, I am grateful to have gained so much in such a short space of time.

 

Shakera Begum at MRC BNDU – Oxford

 

“My impending aspirations have been transformed since this placement and I look forward to what the future holds for me thanks to in2scienceUK”

My placement was with the University of Oxford in the Brain Network Dynamics Unit, alongside Petra Fischer and Eduardo Martin Moraud. I don’t think ‘passion’ is a strong enough word to describe their love for the infamous Basal Ganglia and its role in Parkinson’s disease.

Yes, I too first thought Basal Ganglia was an Italian dish and I couldn’t have been further away from the truth!

During my placement, I participated in several experiments and observed methods for recording or stimulating brain activity during different behavioural tasks. An EEG procedure was one of these, where Petra designed a programme to record brain activity during rhythmic movement to investigate how this activity changes with cognitive load.

In case you were wondering, this cap cannot be purchased anywhere on the high street – I know, what a shame!

The cap was connected to an amplifier in order to record the signals. The same amplifier can also be used to record activity of the basal ganglia from Parkinson’s disease patients to understand their involvement in movement related or cognitive tasks. We were shown different types of oscillations and readings to expect and how to filter a signal, which really just makes the data look clean and pretty.

We also had some fun controlling Edu’s movements with TMS, a tool that is not only used for research but also for example to treat depression. TMS relies on electromagnetic induction to stimulate a focal region of the brain. The procedure involves placing a magnetic field generator or coil near the head of the person receiving the treatment.

Researchers use TMS to measure the connection between the brain and a muscle to evaluate damage from stroke, multiple sclerosis, movement disorders, motor neuron disease and other disorders affecting the spinal cord.

 

As if all these new research skills were not already enough, we conducted a practical regarding muscle movement led by the King of the Spinal Cord himself. Edu showed us how to analyse muscle activity when movement change in speed or when they follow a template or shape in comparison to when freely performed. We observed greater muscle activity when movements were fast and more tightly constrained.

The past two weeks have not only been eye-opening for a new career path and a wonderful experience to learn new skills, but I genuinely feel it has been such a privilege to work with some of the world’s top scientists! I don’t think I have enough words to express my gratitude for the knowledge shared and the hospitality shown by the entire team. My impending aspirations have been transformed through this placement and I look forward to what the future holds for me thanks to in2scienceUK.