Category Archives: Reflections

Personal accounts of research life, visiting a conference, meeting with an inspirational scientist etc

Battle de suprême: CRISPR vs. RNAi based screening

|
Reply

Written by: An Uncharacterized ORF

genome_editing

(Commentators speech log)

Dear XXs and XYs, Welcome to the LoF Screening Championship hosted by the World Federation for Functional Genomics (WFFG). We’re having a gloriously sunny day and a more perfect stage couldn’t be asked for an ultimate entertaining extravaganza. LoF, sounds eerily like ‘laugh’ so you may think that this is a competition for the king of comedy of sorts, the one who can leave you Laughing-on-Floor, but sadly it stands for Loss-of-Function.

Loss-of-function screens are concerned with understanding the function of genes by quintessentially removing them from a cell and observing the consequences. For instance, it has been applied in identifying genes that are essential for survival of cancer cells, with the intention to pick out diagnostic markers and targets for drugs, giving them the ability to kill cancer cells. Similar to other functional genomic tools like transcriptome and proteome profiling, LoF screens have also been adapted to high-throughput settings. By nullifying the function of many genes in one go, these techniques can produce a copious amount of data leaving the analyst melancholically overwhelmed.

Today on stage, we have two contestants both of whom have been adapted for high-throughput LoF screens. While one works by knocking down the mRNAs to suppress gene expression, the other works by knocking the gene out. On this sombre thought of gene annihilation, let’s watch this crown battle for the favourite toolkit of natural philosophers, aka scientists.

But first, here’s a quick look at their bios.

 

RNAi:

Popularly known as RNAi, Ribonucleic Acid interference is the veteran here. Make no mistake, despite the nominal reference to a recreational drug, RNAi’s character remains unblemished by any doping scandals, and most likely is a scornful quip on the scandalous.

Brought out from obscurity by Andrew Fire and Craig Mello in 1998, RNAi generated a huge fire, ahem, fan following and swiftly became the poster child of the Silencer movement that rose to its prominence post-millennium. The arrival of RNAi to the scene provided immense psychological boost to her fans, who could then use it to write their own stories of explorations on suppressing their favourite genes. No wonder RNAi became a heartthrob; for it empowered the people for targeted gene suppression and gave rise to a democratic wave of explorations.

RNAi’s prime strengths are its dicing and slicing abilities that it derives from the adventuring Argonautes. RNAi’s two avatars, siRNA and shRNA, have been successfully deployed by her fans for quite some time. However, as they grew familiar with the technique, RNAi has fallen prey to the old maxim, “familiarity breeds contempt”. Sufficient time has already been devoted to expose RNAi’s shortcomings, inefficient knockdown and off-target effects, that has MELLO-wed the FIRE in RNAi.

 

CRISPR:

on the other side is a new kid on the block. Clustered Regularly Interspaced Short Palindromic Repeats (catches breath) under the nom de guerre CRISPR has ascended to stellar heights within a very short term. Legend has it that, when CRISPR was young and still hadn’t realised his full potential, he was found protecting bacteria in yogurt from viruses. It was Emanuelle Charpentier, Jennifer Doudna and Feng Zhang who trained CRISPR and helped unleash his capabilities.

CRISPR’s strengths come from its Cas9 arm with which it can break DNA at any address directed by the Guide RNA. CRISPR has become a sensational star and has found a cult fan following in the Genome Editors. Ever since CRISPR came into the scene, the Genome Editing community has been very gung-ho about it, almost to the level that their infectious enthusiasm has raised eyebrows of the Human Germline Ethical Brigade.

Like RNAi, CRISPR has also been morphed to perform high-throughput LoF screens. The question remains, who is better at it? Let’s hope we will get the answer today.

 

… Continued …

Originally published at: FIMMSights Blog!

Meet a Bioinformatics student who met “30 Nobel Laureates”

|
Reply

Original blog link:

Meet a Bioinformatics student who met “30 Nobel Laureates”

12391879_10207933806692395_975285434976070417_n 12294837_10207933809652469_4338556901926462767_n 12391338_10207933809252459_4553326795062081779_n 10537762_10204149873616433_809947491673941170_n

  • The Lindau Nobel Laureates meeting with Prof. Walter Gilbert who developed the DNA Sequencing methods
  • Camel ride at the Canary islands
  • Reindeer Safari in Lapland
  • My Master’s Graduation ceremony

Let me first start with my childhood. I was born in Madurai and brought up everywhere. As my father was a bank employee, he used to get transferred every 2-3 years and we had been relocating with him. I studied in many different schools all over Tamil Nadu, which indeed gave me an opportunity to mix up with people from diverse backgrounds. Thanks to my mother, wherever I studied, she encouraged me to participate in all the competitions, which helped me to boost up my confidence.

When I was in my 10th class, we had a discussion about “Which group to choose and where to study?” Well, the direct questions were, if I should become a doctor or an engineer. I actually liked both computer science and Biology. Since we have a doctor (uncle) and 3 pharmacists (grandfather, uncle and aunt) in our family, everyone motivated me to choose biology. After endless discussions, I decided to study biology. So, my fate was decided then and everyone was looking forward to seeing me as a doctor. I was putting my utmost efforts to become a doctor. Unfortunately, my board exam marks were not as good, as I expected. Well, I secured 97.5, but the cut-off that was needed to get a MBBS seat under the government quota was 98.5 back then. Many of my relatives told me to get into some engineering college. Just because, I didn’t get a medical seat, I didn’t want to choose some random course and be happy with my life. My father always says, “Never do something that you don’t like”. I was very stubborn in my decision.

I took a break, stayed home for 1 year and wrote all possible medical entrance tests both at the state and All India level. I also used this time efficiently to interact with as many doctors and engineers as possible. One thing I figured out from their conversations was “They decided to become an engineer or a doctor, just because their parents wanted them to do so or their friends and relatives motivated them or they didn’t know what to do and chose to become an engineer”. After hearing their stories, I decided that I don’t want to be one among the crowd and I should do something different. At that point, I was happy that I didn’t get a medical seat and I didn’t choose some random engineering course that I was not interested in. Just to warn you that this is not the overall statistics. It is my perspective based on the few conversations; I have had with the engineers and doctors. I explored all possible career options with the help of resources that were available online and in newspapers. One morning, when I was having coffee with my father, he told me that he came across a course called “Bioinformatics – Solving problems in Biology with the help of computers”. I got so excited, as I wanted to study both biology and computer science. When I looked into career options for this course, I didn’t find many job opportunities in India. Since I liked the course curriculum, I opted for doing B.Tech Bioinformatics in SASTRA University. This is how I ended up in Bioinformatics.

When you have a passion for something, you will definitely excel in what you are doing. I was very happy during my B.Tech and kept my eyes open looking for opportunities. I went to many conferences, visited industries, attended many research trainings and worked as a summer research fellow.  I enjoyed all these experiences and wanted to be a Master in Bioinformatics.  I was in a dilemma with the questions popping up in my mind, “Where to do Masters? How to promote my career further ?”

When I was doing my 3rd year B. Tech, I got a chance to attend a Career Abroad program conducted by Mr.Sivakumar and Ms.Savitri in SASTRA. That was a life changing experience and I got to know about the Masters’ programs in many different universities across the globe. I was so excited and started preparing for GRE. In the mean time, I got placed in an IT company. I didn’t want to take up the job because I wanted to do masters. But then, the financial situation was not so favorable to start masters immediately after my Bachelor’s degree. Even my parents advised me to take up the job to gain some experience. To be frank, they were afraid to send me abroad initially. After all this drama, I started working with the intention that I will quit after 2 years. Though I took up the job, I used to think every single day that I should study Bioinformatics and shouldn’t work as a software engineer. I couldn’t handle this after 1 year. I made a bold decision to quit my job and apply for Masters.

Though my initial plan was to do my masters in US, I got to know from my friends that there are many exciting opportunities for Bioinformaticians in Europe. So, I sent my applications mainly to the universities in Scandinavia and Switzerland.  I had to wait for 6 months to get the decision from the universities.  I had no clues what to do during these 6 months and approached Shiva sir about getting a position in Trichy Plus. He immediately agreed and I started working there. I would say that this was one of the best experiences in my life. I really enjoyed interacting with students and helping them with their career growth. In fact, this job made me realize that communication skills are my strongest assets. Thanks to Siva sir and Savitri mam for being the mastermind behind the success of many students from Trichy. I feel so great to be a part of TRICHY PLUS.

Finally, after waiting for 6 months I got the admission letters from all the Universities, I applied. I chose University of Helsinki over other Universities because the Masters program is really flexible in Finland i.e you are free to do any course you like during your Masters, including the ones from other departments. Moreover, the quality of education is really good in Finland and it is free. Having all this in mind, I took the major step forward to accept my admission and moved to Finland.

Finland is very different from India, both climate-wise and culture-wise. I was shocked in the beginning. But then within a year, I got adapted to everything with the help of my friends.  Gradually, things turned out good and I got an opportunity to do my Masters thesis in a Pharma company, where I worked on developing new computational methods to assist the design of selective drugs for cancer targets. Overall, I was very happy with my research experience and wanted to continue further.

With the support of my research supervisors, I started a PhD in Computational Drug Discovery at the University of Helsinki in 2012. Even though I have been to many conferences during my PhD, attending the Lindau Nobel Laureates meeting, where I got an opportunity to meet “30 Nobel Laureates” in the field of Medicine and Physiology was a life changing experience. The mind-blowing speeches by the great legends changed the way I think and do research. This was indeed the happiest and the best moment in my life. Though my PhD journey has been quite successful so far, I faced many challenges.  The moment I think that my research is contributing to improve the strategies used in drug design, all these problems disappear like passing clouds.  As a PhD student, I think it’s just the beginning. I am looking forward for much more challenges and opportunities.

In addition to doing research, I have been traveling quite a lot for the past 5 years.  Every trip has been a memorable one, because of the interesting personalities I met during these trips. You learn only by experiencing things and meeting people. Whenever you get a chance to travel, utilize it.

Something that I learnt during these years, “Always pursue your passion. Success will follow you”. Whenever you are confused about making a decision, take a short break, devote some time for yourself and do what you think is right. Sometimes, it is good to satisfy others. But it’s your life. You need to decide, what is good and what is bad for you.

You can contact Vigneshwari at vignesh.bioinfo@gmail.com

https://fi.linkedin.com/in/vigneshwari-subramanian-10931749