Baby Immunologist

Hi Guys and Girls,

I recently came across this journal called “T-scan: A Genome-Wide Method for the Systematic Discovery of T cell epitopes” by Tomasz Kula and colleague.

After reading it, I was so fascinated by the possibility that this technology can offer. Basically this technology takes advantage of the ability of CD8 T cells to secrete granzyme B to target cells upon recognition. What they did was they transduced target cells to express some 2882 amino acid fragments covering the cytomegalovirus (CMV) genome. I should say now that they used CMV because the epitopes are already well-established. So they used CMV as a proof-of-principle

Back to the story. They added a T cell population that can recognise a CMV antigen. They mixed the T cells with the target cells. Once the target cells get granzyme B, they fluoresce. The fluoresced cells are then collected based on their fluorescence, DNA are isolated and sequenced by next generation sequencing (NGS). Indeed, they were able to enrich the targeted epitope, which showed that the method works. They also showed that the technique can be used to identify novel epitopes.

The authors proposed that the technique can be used to apply to other areas in immunology such as cancer immunology, autoimmunity, vaccine design and many other areas.

Source: DOI:https://doi.org/10.1016/j.cell.2019.07.009

Hi guys, in this post I’ll talk about memory responses. Most of you probably know this already but I’ll go over it anyway. In response to an infection (or vaccination) that induces an adaptive immune response, some antigen-specific T and B lymphocytes differentiate to become memory cells. These cells can be found in blood, secondary lymphoid organs, bone marrows, tissues and divide very very very slowly. Should you get infected again by the same pathogen, these memory cells, which have already undergone activation, class switching and somatic hypermutation (in the case of B cells) divide very rapidly. The speed of the memory antigen-specific T and B cells division and activation is the reason why the infection is resolved very quickly compared to the primary infection.

Thus, much like memory in real life where we learn from our past experience which allows us to quickly respond to the present and future, immune cells also have memory.

As biologists, we probably don’t care much about statistics until we actually need to use it, which is at the very end of the experiments or before the write up. I’d made this mistake throughout my degree. Looking back, what I should have done was gain some basic knowledge in stats early one and throughout my degree. This would have made my life a lot easier when interpreting data, write up, reading papers and asking good questions in seminars.

I’m not saying we should read the whole 300 pages or so book on statistics. Read up on frequently-used stats in biology such as T-test, one-way & two-way ANOVA and their non-parametric counterparts, survival analysis, dissociation constant and so on. I assure you that knowing the basics of these stats will make you life a lot easier as a biologist.

Baby Immunologist

Most of us, once we start in a new lab and/or being shown how to do an experiment, we often just get on with it. We follow the protocol to the letter with no questions asked. This approach may work and your results might turn out perfect. However, what if things were to go wrong? How would you trouble shoot?

This is where spending few hours in a library (figuratively and literally) really help. A quick download of NATURE protocol, Springer protocol or from companies could really save your hours of anxiety. Find out what the reagents do and why you add them. A simple google search is often sufficient to give you a background information.

For example, in the case of western blot (or immuno blot), why do you heat the samples at 70 ^oC in the presence of sodium dodecyl sulphate (SDS). Why do you add beta-mercaptoethanol. Why sometime you would block your membrane with milk, while the other you would block it with bovine serum albumin.

The point is, read the protocols. Most NATURE protocols and Springer protocols will elaborate the reasons behind the addition of reagents and certain nitty gritty of the procedure.

I hope this helps young scientists out there.

Baby Immunologist

Today I came across an interesting concept that I may have missed during my degree in Immunology. This concept is the bystander effect in the context of CD8 T cells in response to intracellular pathogens such as Listeria monocytogenes (L. monocytogenes). L. monocytogenes is a gram-positive bacteria that can create an inflammatory environment that can “license” dendritic cells, through toll-like receptors, to express co-stimulatory molecules such as B7, CD40 and 4-1BBL. This, in turn , allows “licensed” DCs presenting L. monocytogenes peptides to directly activate CD8 T cells without CD4 T cell help.

The bystander effect: if you are around, you are in

So what I’ve found was that, in addition to the above pathway, naive antigen-nonspecific CD8 T cells can be activated to produce proinflammatory cytokines when they receive IL-12 and IL-18 made by activated DCs in response to L. monocytogenes or Burkholderia pseudomallei. This allows mice to fight against the infection before the generation and expansion of specific CD4 and CD8 T cells. Thus, it seems like this mechanism acts in an innate-kinda way, helping contain the pathogens at bay before the more effective cell types arrive.

Baby Immunologist

Disclaimer: this article has not been peer reviewed and the knowledge was gained from Janeway’s Immmunobiology 7th edition.

In this article, I’d like to talk about how being arrogance nearly messed up my academic career.

During my A-levels, I was one of the best, if not the best in my biology class. I was able to absorb everything that the teacher taught me. I was better than my peers. I thought nothing in this world could stop me. That was the beginning of my downfall.

For years, during my University and beyond, I refused to accept new learning techniques, tools and guides that would have enhanced my knowledge and understanding of the subjects that I was studying. I wasn’t making use of all the resources available that the University offered. I refused to learn new skills because I thought I was a “genius”. As such, I didn’t particularly do that well in my degree.

After many years, I’ve come to realise that I’m no genius and I need to put a lot of work into my career. Now, I am more humbled, accepted my flaws and doing my best to catch up all the years that had been lost due to my arrogance. So my advice to people reading this post is that, do not lose yourself. Do not forget the reason why you are where you are…..hard work (or lack of), connection, friends and family and resources. Find yourself and you’ll get there.

Baby Immunologist

So I’ve read a part of Janeway’s Immunobiology and found something that I’d not thought about before. Activated T helper cells, even after commitment, still need signals from cytokines in order to continue to perform their effector functions. For example, activated Th1 cells still need a signal from IL-12 through IL-12 receptor and activated Th17 cells still need a signal from IL-23 in order to provide a protective response.

Thus, much like Rafa Nadal still need constant nagging and guidance from his uncle & coach and us scientists still need constant nagging and guidance from our parents and partners, committed T cells still need constant nagging from the their inflammatory environment to perform.

Baby Immunologist

How it all started?

Smart phone is a really useful thing and most of people of this generation can’t live without. That’s right guys and girls, you know what I am talking about. It all started when I started my A-levels (2006) in England. I’d first had access to broadband and I was hooked on internet straight away. I was using Facebook, watching Youtube videos, binge watching movies. Luckily at the time it didn’t really affect my academic performance but I knew I could have done better. The bad habits carried through University, where I was even more addicted to Facebook…..you know….keeping up-to-date with the world and show off my perfect University life. I was also binge watching YouTube videos for hours on end. The bottom line is I was so addicted to it that I spent most of my free-time, time that I could have spent studying, researching and writing my essays and learning useful soft skills.

Postgraduate studies: the addiction continued

Thanks to my short-term memory, I was able to get an overall 2:1 in BSc Biotechnology from the University of Manchester. However, I knew that I didn’t realise my full potential. I was able to enter the University of Oxford to study Immunology and passed my degree with a decent enough mark.

My CV was good enough to get accepted onto a PhD position with a very good research group. However, the addition didn’t stop. Facebook and Youtube were killing my study. The thing is….I knew that these things are bad for me. My brain had been wired to use social media. I could have failed in my first year of my PhD. But I was able to do enough just to get good results and pass my PhD.

Now: The New Beginning

I’d been dealing with my addiction. I’d quit Facebook, Instagram, limited my time on Youtube – only watch videos that teach me new skills that I need. No more binging. I’d started running again after a long time and had ran a marathon. I am now a regular gym goer. So things were moving in the right direction. However, the moment that changed everything was when I came back from my holiday in Italy. I don’t know how, must be the magic of the country (I went to Florence, Sienna and San Gimignano). I made a pack with myself after my holiday that I will come back a changed man. I will focus on my career as a postdoc, make great discoveries and become a PI.

I don’t know what happened to my head in Italy, perhaps things just came together at that moment. Anyway, who cares? Now I’m getting my life and career back on track and I will do my best from now.

Perhaps you have a similar experience or going through something similar? My advice to you is get rid of your social media accounts. Whether by deleting or deactivating. Trust me, life will never be the same….in a good way.

Peace

Baby Immunologist

Hi guys and girls, welcome to the very first “Baby Immunologist” blog post. I will use this platform to walk you through my life as a scientist, the struggles I’ve experienced, achievements, disappointments, motivation and self-improvement to name a few. Another reason for starting a blog post is to improve my writing and communication skills. This is my first ever blog post here. I will be regularly uploading my contents and I hope that you all enjoy reading it.

Peace,

Baby Immunologist