COVID-19 – ⋆ Second Gen Desi ⋆

Pree April 9, 2021

Digestible Science – CD8+ T Cells and COVID-19

Reading Time: 6 minutes

This is a blog post aimed to make technical scientific concepts more “digestible” for a lay audience. The work discussed is based on the research by Kusnadi et al., published in Science Immunology in January 2021. To read their work directly, please click here.

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It’s been over a year since the words lockdown, remote working, and stay-at-home became frequent in our conversations, and we have the global impact of the COVID-19 pandemic to thank for that.

Since then, we have applauded the efforts of fast-acting scientists and pharma in pumping out effective vaccines to help slow down transmission, but unfortunately, vaccine administration efforts have been inconsistent all over the world. Global herd immunity seems like a noble concept, but with conflicting policies and lack of organization among governments, it’s something that will be impossible to reach—at least in the short-term.

But those of us who have been vaccinated are incredibly lucky. Vaccines introduce biological material (based on an infectious agent) into the body to prompt a response from the immune system. If a vaccinated individual encounters the actual infectious agent in the future, their immune system should be able to recognize the foreign invader and prevent an infection from progressing. And of all the immune system’s key players, we have our lymphocytes—our T cells—to thank for this!

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In a previous blog post of mine, I described in general what CD8+ T cells are, but let’s recap:

T cells are born in the thymus (hence the “T” in their name) and primarily serve as “soldiers of the body”. If the body is under attack by foreign particles (often referred to as antigen), T cells are the main players in fighting off these particles to prevent damage in the body.

They are further categorized as “T helper” cells (CD4+) or “cytotoxic T” cells (CD8+). CD4 and CD8 are structures made out of carbohydrate and protein “blocks” and exist on the surface of T cells, giving off their identity. CD4+ and CD8+ T cells differ in how they interact with other cells in the immune system and foreign invaders.

So we know that vaccines can provide protection against viral infections like COVID-19 by introducing T cells to parts of a virus and priming them to recognize the virus in the future. But for those who were infected with COVID-19 directly, did the intensity of the symptoms they experienced alter their immune system at the cellular level?

A collaborative group of scientists out of San Diego, California and the United Kingdom believe this was something worth investigating, and went so far as to use advanced genetic sequencing techniques to conclude that when it comes to our immune system warriors—CD8+ T cells—the severity of COVID-19 symptoms could affect how these cells look and function. Their work was recently published in Science Immunology, a prestigious peer-reviewed journal in the immunology field.

Article by Kusnadi et al. recently published in *Science Immunology*

Since CD8+ T cells are critical when it comes to vaccine effectiveness and understanding immunity, it would make sense to characterize how CD8+ T cells are affected by COVID-19 infection. Obviously at the time this study began, not much was known regarding this, or much about COVID-19 in general.

The authors used blood samples from healthy donors, COVID-19 patients that were not hospitalized (characterized as ‘mild disease’ patients), and those that were hospitalized (‘severe’ patients) to isolate peripheral blood mononuclear cells (PBMCs).

PBMCs hold the key players of the immune system—T cells, B cells, natural killer (NK) cells, and monocytes—and are characterized by their round nuclei. Isolating this layer from the peripheral blood makes it easier to analyze CD8+ T cells in particular.

To isolate CD8+ T cells from the PBMC samples of COVID-19 virus-affected patients, the authors used a “cell sorter” to specifically collect CD8+ T cells expressing CD137 and CD69. Both of these markers indicate CD8+ memory T cells that are activated and are ready for battle. Going back to my earlier post, tacking the word ‘memory‘ next to CD8+ T cells indicates that these cells have the ability to recognize and act against a foreign invader.

Interestingly, the expression of CD137 and CD69 was increased in CD8+ memory T cells derived from “severe” COVID-19 patients compared to “mild” COVID-19 patients, perhaps indicating that severe patients could have an increased protective response to COVID-19 antigens in a future encounter.

A very basic and cartoonish depiction of activated CD8+ memory T cells in mild and severe COVID-19 patients.

Even though the analysis becomes more complex as the paper continues (given the nature of genetics-based techniques), there is no need to feel intimidated. There are still key take-aways from the paper that even someone with a non-scientific background would appreciate.

Depending on the viral infection, CD8+ memory T cells can respond by activating a number of different genes that can help with fighting back at the infection. For example, COVID-19-reactive CD8+ memory T cells were observed to express genes associated with exhaustion, the production of molecules (cytokines) that assist with fighting off infections, and activating T cells.

“T cell exhaustion” is exactly what it says—when T cells lose their ability to fight off infections due to non-stop stimulation by a foreign invader, they tire out and do not function optimally in their normal defensive roles. A common marker of “exhaustion” is programmed cell death protein (PD-1) which T cells can express on their surface. The issue is that PD-1 is also involved in the activation of T cells, so like most things in biology, it’s not black and white—there needs to be a balance.

The authors knowing this utilized single cell transcriptomics, a process that allows us to examine all sorts of genes expressed by an individual cell, to see if there was more to characterizing exhausted T cells beyond what is seen at the surface level.

Ultimately, they found that CD8+ memory T cells reactive to COVID-19 expressed a number of genes associated with exhaustion, because of their connection to type 1 interferon signaling. This cell signaling pathway is associated with immune system regulation and has been noted by earlier studies to be linked to the development of exhaustion in T cells.

A simplified version of a “cluster map” and a “heat map”. More advanced depictions of these plots can be used to assess how genes group together in a particular sample and if they share similar functions.

Although patients with mild disease had more exhausted CD8+ memory T cells compared to severe disease patients, the exhausted CD8+ memory T cells in severe patients showed an increase in the number of genes associated with toxicity and inflammation.

Even though we would see this as a “negative” attribute of severe infection, it was noted that those with severe disease had CD8+ memory T cells that could survive for a longer time, although whether this observation can provide long-term immunity still requires investigation.

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Given that this is a study involving live individuals, using PBMCs is the only way to go, even though the analysis can be limiting (we can’t exactly do lung biopsies willy-nilly!). Even with its limitations however, the overall study does bring valuable insight as to how CD8+ T cells are affected by mild vs. severe COVID-19 infection.

The authors were able to use techniques to isolate single CD8+ T cells reactive to COVID-19 and determine that although patients with mild disease have more CD8+ T cells that are exhausted, the exhausted CD8+ T cells that severe patients do have lean towards higher levels of toxicity and inflammation, despite these cells also exhibiting features of increased memory responses and survival…

Maybe in this case, quality does take precedence over quantity? It will be interesting to see if any follow-up studies are conducted based on the findings of this paper, as we still have so much to learn about COVID-19. Although I do think it’s safe to say the authors uncovered some interesting details on how COVID-19 infections impact our immune system’s essential soldiers.

This has certainly been a lot to digest, but it was a delicious meal of brain food to dive into!

Resources cited in this post:

Pree March 9, 2021 Milan, Italy

Day by Day

Reading Time: 10 minutes

Before that night in late spring of my junior year of high school, I could not comprehend how painful a mental breakdown truly was.

I played singles varsity tennis that fall. I had been awarded the position of first chair flute in county honor band that winter. And that night, I had completed two regional competitions for Robotics as president of my high school team, bringing home an award for our website as well—-something that had been a personal project of mine finally received validation, yet it triggered my anger.

Logically, I had nothing to “cry over”, yet the dark idea that it would all come crashing down triggered the tears, guttural yelling, and body slams against the floor of my parents’ bedroom.

My mom with her own mental illness, fueled the fire with her share of yelling and ridicule that I was the one that needed help. My dad, shocked at the scene going on before him and unable to stop my incessant crying and self-harm, threatened to call the police.

But this only pushed out more tears, and at one point, my body couldn’t take it anymore. I continued to lay on the floor listlessly while my parents calmed down as well.

The police never came, but Dad thought I should see a therapist. I was resentful, given the fact that my mother had not seen a doctor in years, but part of me felt the urge to see someone, with a sprinkling of curiosity.

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I have lived with depression since then, with it popping in and out of my life at varying intensities, depending on how kind my environment was to me.

An eating disorder was mixed in as well, sometimes making it unclear what was first to influence what.

The depression, along with OCD tendencies, popped up along my PhD journey as well, with one of my darker episodes occurring at a time when so many unknowns were at play… the biggest of which was the worry of how soon my first, first-author paper would be published, if I would be able to graduate, and if it was even worth all of the anxiety and emotional breakdowns I was going through.

It was around this time I decided to see my third therapist, but also consider taking medication for the first time. When I received the news that my paper had been accepted, that itself lifted away the weight of the world that was pressed so firmly at my shoulders for the past six months, but I still felt it necessary to seek out professional help.

Dr. S was an immense help through the first half of 2019. It may have helped that my environment suddenly turned friendly, but she helped me battle the ennui I was now experiencing as I inched towards a summer graduation.

At first I saw her once a week so she could get to know me better and monitor me as I started taking Lexapro for the first time. I was on 5mg initially, but was bumped up to 10mg. Beyond a few headaches and fatigue, the pill got acquainted with my body and lifestyle, although I personally didn’t feel any changes.

Especially since I still felt cyclical anger and irritability.

Dr. S was a trained psychiatrist, but would not continue writing prescriptions for patients unless paired with counseling sessions. I enjoyed our sessions in the beginning, since I was able to vent to her about my desire to start anew outside of SoCal. She knew about my plans to apply for a fellowship in Italy, and how I yearned to have the opportunity to meet new people and travel all over.

When my plans were starting to gel by November 2019, I began to grow tired of my sessions with Dr. S. Like with the therapists of my past, I had hit a plateau with her. I felt like I didn’t need her anymore, and that my depression had retreated once I received confirmation about Italy.

Of course with COVID in early 2020, my plans changed dramatically. I was “stuck” in Tulsa (although now I see it as a blessing I wish I could relive again). Being with my family definitely played a key role in mitigating stress. I was still taking my Lexapro, but popping a pill each day without knowing if it was truly serving its purpose was beginning to irritate me, to say the least.

Dr. S wrote me a prescription for 90 days to take with me as I settled down in Milan, but who’s to say if it got me through my two weeks of isolating self-quarantine?

Because my mind was already set on starting fresh and throwing myself into a different world, I felt ready to stop the Lexapro. I didn’t want to rely on medication to modulate my mood for the rest of my life, especially if it wasn’t doing its purported action in the first place.

Things seemed to be going wonderfully at work.

I was finally opening up and starting to date for the very first time in my life.

In fact, I was lucky to meet someone so early in the “game” who I clicked with instantly.

And with all of this new-found happiness, I wanted to see what my body could do on its own…in an environment where I felt in control and eager about navigating through.

So I stopped taking Lexapro in mid-August 2020. I informed my Dad and a close friend of my decision, both of whom knew of my recent depression history. My Dad, knowing the obstacles I have faced when it comes to doctors and their diagnoses understood why I chose not to wait until I found a doctor, but my close friend was more concerned. While I acknowledge it would have been helpful to see someone within weeks of arriving in Italy, I knew that with the painfully frustrating administrative system in place—especially in regards to healthcare—it would have been a nightmare to wait for a second opinion.

In my battle with depression over the years, I quickly realized that when it came to my body and mind, only I could be the one to decide what felt right for me.

I felt “normal” for about a week, after which painful, throbbing headaches began to make an appearance on a daily basis. I was starting to feel easily triggered by what I would normally see as minor inconveniences. On my early morning runs, I would have to stop mid-run because I would be on the verge of tears…

Things started to feel uneasy at work. I found myself silently hyperventilating at times, and I often had to duck into the bathroom to let myself had a good cry.

I knew fully well I had nothing to be upset about. I stopped taking the medication because things were going well. I wasn’t too concerned about these symptoms arising because I was expecting them as part of the withdrawal process.

Everything would be better in a few weeks…

But it seemed as though things were slowly retreating and heading in the opposite direction. The throbbing headaches did stop after three weeks. I wasn’t crying uncontrollably everyday either, but my mood was no longer at the same elevated level that it has been in mid-summer.

And perhaps it was because my environment, the one I thought I had control over, was starting to become more overwhelming than I ever imagined it would be.

Having the patience to learn and speak Italian was becoming a stressful chore.

Work was becoming something I was slowly starting to dislike. I resented the idea that my position wasn’t as flexible as I thought it would have been. I felt like my skills weren’t being appreciated. And having these feelings woven through a five-day work week was an feeling that grew unbearable by the minute.

As fall turned into winter, I thought time would make things better, but with the rise of COVID infections, we were back in a lockdown in late October. I was resenting the fact that I had yet to travel outside of Milan or Como, and I was counting on the winter holidays to make my Rome trip a reality.

But that of course didn’t happen.

At least I wasn’t alone during the holidays, but my anxious thoughts and depression still would not leave me, even though I knew I had a full week off from work to take in the last of 2020 (although, what was really there to take in?).

I kept thinking about how I was “wasting” my time off because I wasn’t able to travel. Or ruminating over what experiments I should be planning my first week back at work, even though that was the last thing I wanted my thoughts to dwell on…

Castel Baradello hike the day after Christmas. It was a beautiful sight, but my mind was gripped with anxiety about my week off ending soon…

And with the arrival of 2021, things still seemed to not “feel” any better. Yes, I was finally able to move into apartment that wasn’t the size of a claustrophobic closet, and with a balcony (something that was a top priority), but I still felt unsettled 😔

I thought I would appreciate a long, cold winter after months of painful humidity and encapsulated heat, but I guess I didn’t know what I was asking for when it came to an Italian winter. The weather became piercingly cold, and the sky always seemed to match my mood—gray, dreary, tired, depressing…

I tried to keep my mind away from the gray by appreciating things I knew would bring me joy.

Like, (finally) buying a Nespresso machine so I could have coffee on my terms.

Or stopping for adorable cats that ‘meow’ back and don’t mind being coddled.

And even trying to shift back to daylight runs vs. the nighttime runs I had a habit of partaking in during the summer. Because every ounce of sunlight helps.

Work continued to aggravate me. I still felt like I was doing tasks that weren’t adding to my skill set, and that what I was doing had no relation to what I thought I had signed up for.

Looking back, I find it ironic that in the phone calls I had with my Dad during this time, I’d semi-joke about having a breakdown at work given all the emotional turmoil that had been building up for the past several months.

And, then it happened right on cue 🙃. Before I broke down into a solid cry that drenched even my blue disposable mask, I was having a meeting with my boss, during which she expressed her disappointment with how things were going (I would later learn that she had been described by others to push people to their breaking point in an effort to get the most work out of them). I didn’t have the energy to explain my situation, so I let my emotions do the talking.

She seemed to understand immediately, and offered help where she could. At least that situation got me into a doctor’s office for the first time in Italy 🙄. I knew counseling had helped me in the past, but this time, I already knew what my trigger was.

A stressful, overwhelming environment.

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Since my breakdown as a junior in high school, I have accepted that depression will always be a condition in my life, and that it may need managing from time-to-time.

When I felt out of control with where I would be going to college and troubles at home with mom, diving into an eating disorder was my solution.

When I felt deep anxiety about the fate of my PhD, and the paper I was anxiously trying to publish for a timely graduation, Dr. S and my willingness to try medication for the first time was my solution.

And I thought Italy would be a long-term solution. Especially for the irritability and ennui that popped up in recent years, but it turned out that Italy was an issue of her own.

COVID has been an obvious key player in this, and it’s hard to say how things would have turned out if I had arrived in Italy back in early 2020 as originally planned, and if the world had not been shaken by COVID.

But ongoing events have made me realize that the biggest trigger of my current depression “flare” is directly associated with the very reason I came to Italy in the first place. And how do you manage and cope when the very thing that is your livelihood causes so much distress?

Recently, I’ve been fortunate to have possibilities open up. Knowing that there may be a way out has put my mind at ease, but at the same time, there’s no guarantee that the solution to cutting myself off from the triggers here will help me somewhere out there.

That’s why I’m trying my best—with whatever ounce of energy I do have—to take things day by day. Making sure to sip my coffee, savor a relaxing dinner at home, and pet that furry cutie before each run…

When it comes to using medication to manage my mental health, I personally do not want to get near it ever again. I’m sure it works wonders for some, but that doesn’t mean it works favorably for everyone.

Managing my depression has led me to prioritize my happiness no matter what. I acknowledge that what I may constitute as happiness right now in life could change over time, but even so, I believe that if we make it a priority to live in ways that ensure balanced levels of happiness, we can encourage the same from those we interact with on a daily basis.

An infinite loop of happiness, wouldn’t that be nice?

Looking down on Como from Castel Baradello, two months after Christmas ❤

Pree February 16, 2021 Australia

Guest Post: Connecting Beyond Conversations – South Asian Community in the Midst of COVID-19

Reading Time: 3 minutes

I’m pleased to present a guest post by Joseph F. Kolapudi, a fellow second gen desi based in Australia! When Joseph reached out to me eager to share his thoughts on how connection in our community is essential—especially during challenging times like a global pandemic—I couldn’t refuse. I’m thrilled to feature Joseph’s piece here on Second Gen Desi—it’s definitely worth a read!

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Community. It’s what brings us together in the toughest of times. During natural disasters, world wars, political unrest – it can be the anchor we look for when we are overwhelmed in a sea of anarchy. However, what happens when the one thing we take for granted is distanced from us?

During these days of what can be described as some of the most uncertain circumstances, our current situation in which we find ourselves seems to be a reality that is too hard to understand. But challenging times seem to be the only constant of our present age.

Conversations, especially ones that cross borders, cultures, and caveats to enter into the homes and living rooms of our existences, especially for second generation desis, can be some of the most engaging and most honest conduits of truth that we cling to in these tough times.

I recently connected with a fellow second-generation desi who had been struggling due to COVID-19. Despite our differences in time zones, country borders and situations, I understood the importance that our shared connection had in making them feel valued and appreciated. Although our connection was limited by these factors, we still had commonalities that we could express and seek to understand together. Fast forward to the present day, and she managed to move to the same city, and I was able to connect her to a wider community in which she has now found greater solace and similarities.

These are the conversations that we have a hard time engaging in, especially in the midst of a global pandemic. Though cultural conversations have been a hallmark of our times, what happens when those conversations turn inward towards introspection?

Personally speaking, it’s something I’ve been doing a lot of lately. About how second generation desis can learn to code-switch without even thinking twice, but wonder why others can’t do so without thinking about it long and hard. How we can know a person’s ability to connect with those like us, but we somehow find it increasingly difficult to decipher where they feel more at home. How some people can look past a person’s background or status, but fail to see the struggle despite the façade of success.

We need to look at how we can take our conversations from small talk to street talk. From a person-to-person experience to a communal reality. From connections in a corner of the community hall, to one that’s a worldwide phenomenon that every desi can resonate with in their own, unique way.

Our world is hurting right now, but there is a hope that what lies beyond tomorrow is worth fighting for. It begins with honest conversation, but it doesn’t stop there. Through our own, personal connection to others, we can see the light that God has placed inside each of us.

We can be the community that comes together for true connection; and it starts with us.

Joseph is a second-generation desi currently living in Australia. He currently works as a Project Director of a nonprofit by day, and a cultural connoisseur of Indian cuisine by night.
He also loves exploring different cultures and countries whenever he is able, and recently returned to India for his wedding. As a writer by profession, he prefers to explain stories
through the written word, and looks forward to connecting with the wider desi diaspora!

Pree December 11, 2020 Milan, Italy

T Cell Tidbits

Reading Time: 7 minutes

2020 has been a prime year for immunology, there is no doubt about that. Though recognized as one of the most complex, yet all-encompassing topics in biology, immunology has squeezed its way into the limelight, thanks to COVID-19.

You may have come across these words recently…

Virus.

mRNA.

CRISPR.

Cytokines.

T cells.

Funny how these words were once part of a private exchange between my dense biology textbooks and I, muttered over and over until the concepts gelled in my brain just in time for Advanced Cell Biology exams in the first year of my PhD.

Now they’ve made their way to celebrity status—gracing social media feeds and TikTok videos.

But as a scientist working in the immunology field myself, I cringe when I see posts that have not been fact-checked, or twisted definitions of basic biological concepts circulating in the mainstream media.

Before diving into all the COVID-19 articles out there (many of which are based on publications that have yet to be formally peer-reviewed), let’s get some things straight.

Like, what’s a T cell anyways?

T cells are born in an organ snugly fit between our lungs, the thymus (hence T cells), and are categorized as players of the “adaptive immune system”, which makes sense since T cells are quite the malleable bunch. They adapt to the surroundings of their biological environment, and play a critical role in maintaining immune homeostasis in the body.

T cells have the capacity to develop specific receptors against foreign particles, signaling other players in the immune system to fight off burgeoning infections, while also having the potential to remain in the body for years, ready to fight back in case those particular “foreign” particles enter the body again.

They are further categorized as “T helper” cells (CD4+) or “cytotoxic T” cells (CD8+). CD4 and CD8 are structures made out of carbohydrate and protein “blocks” and exist on the surface of T cells, giving off their identity. CD4+ and CD8+ T cells differ in how they interact with other cells in the immune system and foreign invaders.

CD4+ T cells rely on the help of other immune cells (like B cells and macrophages) to fight off infections. Their ability to secrete particles called cytokines (imagine a cell sneezing onto another cell) helps to activate these supporting immune cells so that they can go on to kill the infectious source.

A simplistic diagram of a CD4+ T cell interacting with a B cell, “sneezing” out cytokines like IL-2, IL-4, and IL-5 to “stimulate” B cells to fight off infections.

CD8+ T cells are more precise in their function, since they are able to kill cancerous cells and virus-infected cells directly. They secrete cytokines as well, two of which are IFNy and TNFa, that can help to destabilize infectious cells and tumors.

Within these two categories, we can break CD4+ and CD8+ T cells down further into three sub-types (though there are more sub-types, the following are the most general).

Naïve T cells are the least differentiated of the three, waiting for the day they can respond to a unique pathogen and develop a specialized functions.

Effector memory T cells (T_EM) are rapid-acting and ready to respond to foreign antigens (think, unwanted floating pieces of protein from the “bad guy”), since they are circulating in the blood or housed in non-lymphoid tissues that may be exposed to foreign antigens immediately (like the skin, gut, or lung).

Central memory T cells (T_CM) are more stagnant, residing in secondary lymphoid organs, like the spleen or lymph nodes, unless stimulated by a foreign antigen—after which they can proliferate into an army of effector cells to enter battle.

This is one way we analyze T cells in the lab. Within CD4+ or CD8+ T cells, we can further distinguish the memory sub-types with the markers CD44 and CD62L.
CD44+CD62L- are effector memory T cells.
CD44+CD62L+ are central memory T cells.
CD44-CD62L+ are naïve T cells.

In the lab, we can assess the markers for these T cell sub-types and their cytokine production to determine if a stimulus of our interest (i.e. a potential cancer drug) can help a T cell to be more effective in fighting off infections. The idea has been a prime goal for many immunology-based labs for years.

Faster-acting T cells should also get rid of unwanted, foreign invaders in the body faster, right? Fast is a relative term, and unfortunately in the world of biological science, nothing is ever fast enough.

Still, we do our best to mimic how a T cell functions in real life (or, in vivo as we fondly refer to it) by activating, stimulating, and measuring markers that help further identify a T cell’s function.

In the lab, T cells are often obtained from spleens of mice and grown in culture (a.k.a. in vitro—imagine a large, nutrient-rich suspension full of blob-like shapes, swimming without abandon—those are cells in culture).

T cells can be activated by a number of ways, but activation via CD3 and CD28 is one of the most common ways to do so.

Just like CD4 and CD8, CD3 and CD28 are proteins that are expressed on T cells and are involved directly with activation. CD3 is part of the prime T-cell receptor (TCR) complex and when stimulated with CD28, can lead to the activation and expansion of T cells.

We’ve got the TCR that includes CD3. We’ve got CD28. Let’s get activated!!!

This process normally takes about 2-3 days in the lab, and we can perturb this process by keeping cells in the presence of increasing concentrations of a drug during activation. Depending on the goal of the experiment, T cells can be grown in the presence of this drug for longer periods of time, and we can select different time points to collect cells and measure markers of their present “identity”.

Simply put, we collect these cells at a given time, count them under a microscope, and then proceed to stain them with fluorescent dyes that are bound to the markers we are interested in.

An example of a panel used to assess the characteristics of T cells in real time! This is made possible by Fluorescent-Activated Cell Sorting (FACS) technology!

Remember IFNy and TNFa? When we stain cells, we can add antibodies that are bound to a fluorescent probe that targets these cytokines. Same for CD44 and CD62L, which are prime markers for identifying effector or central memory T cells (as you saw earlier😉) .

After staining, we analyze the presence of our markers of interest using a tool called Fluorescent-Activated Cell Sorting (FACS) , which is able to isolate single cells and sort them by the fluorescence they give off.

It can be a tricky thing to configure at first, but once you know what you are looking for, it’s an exciting sight for an immunologist to look forward to:

We can isolate particular cell populations from others before diving into our markers of interest. Here, we are “gating” for where the T cells should be.

Next, we try to isolate **single cells** (which is what the green rectangle is gating). The reason for doing so is to prevent “sticky” cells that may make the analysis inaccurate. It is possible that one cell could be attached to another and “slide along with it” during the sorting process, giving off a false reading.

When it comes to T cell function and optimizing it, T cells can be transduced, or have DNA introduced into their system via a virus. In this way, T cells can be “engineered” to express certain receptors on their surface if they come into contact with a specific antigen.

In the images below, we are measuring how many CD8+ T cells are also expressing the VB9 receptor after the transduction process with the SV40 virus.

I’ll keep it simple here because otherwise I may get into another blog post within a blog post 😅…

In this plot, we expect very few CD8+ T cells to express VB9, since they were untransduced.

Q2 is where CD8+VB9+ cells *should* be. We don’t expect too much from cells not transduced with the SV40 virus.

But look what happens after a “successful” transduction (look at Q2):

Boom. Plenty more CD8+ T cells expressing VB9 as well!

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There is absolutely no way all of immunology can be covered in a single blog post, let alone T cells, but having a basic understanding is a perfect place to start. The basics are important when it comes to figuring out if what the media is telling us is sensible versus sensational.

And as a scientist in the throws of it, I also come across the other extreme: the demand to read countless of peer-reviewed papers that are dense, distracting, and rather than furthering the field, make it all the more confusing!

Science doesn’t need to be intimidating or exclusive, but it can certainly feel that way given the immense amount of information out there and figuring out how to sift through it all.

The important thing is to keep an open mind, and don’t be afraid if you are not understanding the story before you—in fact, feel free to question it, because ultimately, that’s what science is.

If you found my tidbits on T cells interesting, I recommend these links for more simple as well as some in-depth reading!

British Society for Immunology

Cells | British Society for Immunology

T-cell activation | British Society for Immunology

Wikipedia

CD4+ T Cells

CD8+ T Cells

Naive T Cells

T Cell Activation via Anti-CD3 and Anti-CD28

T Cell Activation via Anti-CD3 and Anti-CD28 | Thermo Fisher Scientific

Scientific Review

Central Memory and Effector Memory T Cell Subsets: Function, Generation, and Maintenance | Annual Review of Immunology (annualreviews.org)

Pree August 7, 2020 Tulsa, Oklahoma

Life, in the time of Corona…

Reading Time: 8 minutes

Written: June 2020

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The COVID-19 pandemic is something everyone living on this earth currently will have a story for. Shared frustrations, sadness, lessons learned, and renewal are only a few things we will be seeing documented in copious books, documentaries, social media captions, TV shows, movies, and blog posts (like this one) to come.

For me, corona initiated a transition for the world that was in line with my life’s transition. Of course, corona has significantly delayed my sojourn to Italy, but it also brought with it an opportunity to work remotely without the usual stressors, and to spend an indefinite amount of time with family. Things that I am especially grateful for.

Despite the impending doom, I took solace in the rising sun above Fullerton train station’s parking lot in the few weeks before obliging to work-at-home orders. Despite feeling weary at that time, I found a renewed sense of energy from the SoCal sun.

In the weeks leading up to stay-at-home orders and lockdowns, I already felt uneasy—in my living space at the time, the uncertainties of my work visa for Italy, and the emotional ennui of my life in general. Here I was, eager to start anew in a foreign land, ready to make friends and forge new relationships while advancing my career, when the one thing that gets in my way opposes all of that.

My last weekend in SoCal for an indefinite amount of time, and my heart was hurting. For about one hour that Sunday weekend, I was able to forget about it all and allow the beauty of Upper Newport Bay seep into my soul…

Given my life circumstances at the time, I got the okay from by boss to work remotely since my current lab work conveniently allowed for it. And knowing the tribulations of my living situation, my Dad was eager to have me stay with him for a while, and I was more than happy with that—even if it meant taking a hiatus from Cali things and joining him in Oklahoma.

Los Angeles looked so forlorn anyways…

DTLA on a Wednesday morning. Unbelievable…

I spent the first week of LA county’s stay-at-home order moving things out from my residence at the time and wrapping up as much things as I could in-person in the lab. In late March, I arrived in Tulsa, on a lucky flight that hadn’t been cancelled…

I felt so relieved to be in a place where I was free to be myself and feel safe and comfortable for the first time in a long time. However, it took me a while to really get used to the whole idea that everything would be shut down/restricted. It got to the point where even tennis courts were chained up, which came as a disappointment to my Dad and I.

At least the outdoors weren’t “cancelled”.

In the earlier weeks of corona, my Dad and I spent a good amount of time getting “lost” on hikes on local trails, like Turkey Mountain.

Turkey Mountain is a whole ‘nother world on the outskirts of Tulsa. It’s a protected local wildlife/trail area, and even though we made our hikes at high noon, the trails had a fair share of bikers, dog walkers, and runners—conscious of abiding to the 6 feet apart ideal.

Fortunately, I was able to make a lot of time for running during this time, but of course, not without nagging Achilles’ tendon pain, plantar fascitis, and other aches/pains. But because this was a rare opportunity of having “extra” time to devote to fitness, I wanted to make sure running was a priority again.

Speaking of running, this was the first time in all of my Tulsa visits that I managed to run consistently in other places besides Riverside (another local trail that is popular). I found my favorite running route to be very close to (my parents’) home.

A) Because there is something about long, distant roads that makes a runner’s heart swoon,

and B) the animals one runs into are A-DOR-A-BULL (get it? 😅)

I’ve stopped for more dogs, cows, cats, goats, rabbits, caterpillars, butterflies, and spiders mid-run than ever before 😂.

When you think of Oklahoma, hills and mountains don’t really come to mind, but the La Fortune Park area in Tulsa is full of them. The park itself is hilly, so it can serve as the setting for some awesome hill repeats.

La Fortune Park (my favorite side of the park lol)

The park is right next to St. Francis Hospital, on Yale which is literally a giant hill. I like running up Yale, and crossing the street onto a huge green lawn. If you make it to the top, you’re in for some nice views of the city.

Staying with family also meant constant access to home-cooked meals. So grateful for a Dad who enjoys cooking, as much as he loves sharing morning coffee, mid-morning PB&Js and more coffee, and tea and mini samosas before heading out for evening tennis games or walks.

Felt like I was home from college for the 3 months I was staying-at-home with family.

As time progressed during the stay-at-home orders, I wasn’t sure how things would ultimately be for me eventually…yes, I had plans for Italy, but I had my days where I doubted if that was going to even happen. April was just a chaotically somber month on a global scale…

All that running in April also led to a bad Achilles tendon injury in my left foot, which made me turn to a local podiatrist for laser therapy. It was an annoying 6 weeks of having to deal with nagging pain on runs, and limiting mileage in general.

Though that didn’t stop me from having fun on the runs I did go on that month.

On a path to Veteran’s Park in Jenks, OK

Despite the nagging pain, the doc said it was OK to continue running if I watched my mileage and pace. I took this as an OK to continue on with my exploratory nature, running a reasonable distance to local parks and back.

“Jumping for joy” at the beginning of a “new-to-me” trail.

Veteran’s Park ended up being one of my favorites since I ended up befriending two ducks and a geese family—momma, poppa, and a fuzzy babe!

As weeks wore on, I got used to the lifestyle I was living, the routine I had, and the flexibility of my schedule. So much so, that when I finally got confirmation about being able to plan for Italy again, I started to feel a tinge of heart-brokenness. Life was picking up again, but it was going to break my heart to leave my Dad after such an unexpectedly long, (mostly) blissful stay.

The week before leaving, we drove down to Texas for some personal errands, but also used it as an excuse to meet up with my sis in Austin—since with Italy back on the table, I wasn’t sure how soon I’d be able to see her again!

We were only with her for about 3 hours in the evening, but we got plenty of things done during that time—like, acquainting ourselves with her cat Autumn, and having a to-go vegan dinner from Counter Culture, which we ate outside at a picnic table in horridly humid weather, accompanied by mosquitoes…

(Left to Right; Top to Bottom – 1) Hangin’ with Miss Autumn, 2) Dusk views of UT Tower, 3) I can see the Texas Capitol?, 4) TURTLE POND!, 5) CAMPUS CAT!, 6) UT Parking Structure because why not…)

It was a short, but sweet evening. I felt a little depressed after we left my sister, since I knew my stay with family would be coming to a definite close. It’s the biggest tease life can throw at you—the opportunity to stay with loved ones for an indeterminate amount of time, followed by an abrupt parting.

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Before corona, I was exhausted with life. I was tired of Los Angeles. I was tired of being surrounded by people who lacked ambition, and those who constantly complained about what they didn’t have. Their selfishness and callous attitudes were rubbing off on me, and my tolerance for human beings was at an all-time low. I found solace in spending time with shelter animals because they lifted my mood back up after a hard work week.

I was looking forward to leaving for Italy because in my mind, it was a ticket to a new, exciting experience. I was craving adventure in all aspects, and I wanted to drop everything and just fly over!

During corona, I put all of these thoughts on hold. The circumstances initially fueled my disgust for humankind further. I felt like there was no hope to be had in people. I was fortunate to be able to work remotely and live comfortable with family, but not knowing the outcome of anything was aggravating, to say the least. Seeing the cases rise in Italy for weeks was discouraging. I had days that I pondered over “back-up plans”. I put learning Italian “on hold”. Motivation was at an all-time low…

After (?) corona (perhaps I should say, when Italy was ready for me…), I had to put my big girl pants on again. After spending almost 3 months of quality time with my Dad—something I hadn’t done since 2013/2014 before starting my PhD (!!)—I was not enthusiastic about going out into the world again…especially one that was battered by the aftermath of a pandemic.

The truth was, when people asked me afterwards if I was “SUPEREXCITEDABOUTGOINGTOITALY?!”, my heart wasn’t in the “yes” that was my reply. Obviously, months of unplanned events had an effect on my thoughts and outlook for the future.

My enthusiasm would take time to grow again, and I had to accept that. At least I had my good health in all of this 💛.

How has the COVID-19 pandemic changed your outlook on life?