Mental Fatigue in a PhD

Anyone doing a PhD or other graduate programs would be aware of the startling and concerning statistics regarding mental health and students and while there is much more awareness about this everywhere there are still some major hurdles every student has to overcome.

What I am feeling at the moment is what I am calling mental fatigue.

I have been doing my PhD for nearly two years now, and since I started I haven’t had more then a couple days off in a row and recently, I have been into the lab every day for the last two or three months. Sometimes it is not for more then a couple hours, but it adds up…especially when I look at my bullet journal and see everyday has some hours shaded in that I have spent at the lab.

While I do like what I do and love my project, it is tiring and ethically, I have to go into work on those days to check on my animal experiments so I unless I have no daily checks to do, I am always down in the basement collecting more data.

I also went straight into my PhD from honours, having about two months break and the most recent holiday was a weekend in Melbourne which was amazing but over a year ago and I have certainly earned myself at least a couple of weeks of holidays with all of the long days, nights and weekends in the lab. I am planning to head to America over the Christmas break and I am excited (I have yet to ask my supervisors though :/ )

But I digress, I was supposed to talk about mental fatigue which all of the above, plus the usual high workload and pressure that comes with a PhD has lead to me feeling very unmotivated for the last two weeks.

I had just finished a major experiment that required nearly two months of animal monitoring (half of that involved daily checks too), weekly flow cytometry staining and analysis and on top of the other three major experiments I am working on. I have collected some interesting data but the next steps is to repeat the major experiment in a different cell line and set up an even more complex experiment to work out some mechanisms. I am so excited to see what we find, but thinking about how much work it will be. Especially as the honours student who was assisting me with the majority of the monitoring will be finished soon. I also have to finish my review paper that is nearly two years in the making (and I should have published it last year) and stress about getting some extra things on my CV for future post docs and fellowships.

So this week I haven’t had the most productive of weeks. I have slept in until 9 am every day but Monday (and the only excuse is that on Monday I have my fortnightly supervisor meeting) and got into the lab at 11am. Today I left at 2:30pm as I felt so uninspired sitting at my desk and had gotten my lab work done and planned some next steps.

I have not done any more work on my review, read any papers and just feel like everyone else is doing so much more then me. I will also be at Jury Duty next week (I have no idea how long it will take) so next week feels like i’ll not accomplish much either.

But I am recognising that what I am feeling is normal and to be expected considering how much work I have put in. I treated myself to some lunch and coffee at a cafe to come up with a plan…while watching the office for the first time. As i’ll be in and out of the office next week due to Jury Duty, I’ll give you an update in two weeks time to see how I am going and share with you all what I did to try to overcome this.


Please let me know if you are a student, or were a student, or know a student who has gone through this or is tackling this at the moment. I would love to hear how other people deal with this and also other peoples stories!

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Pharmacy (F)Phriday- Cyclophosphamide

First of all, if anyone can come up with a better name please let me know! Titles are 100% not my forte. It always takes me ages to think of a good title for presentations, posters and the one paper I am currently writing!

I am super excited to start this weekly feature on my (very neglected) science blog, titled ‘Pharmacy Phriday’ until someone suggests a new name. Each week I am going to feature a different drug or reagent I use in my day to day laboratory work.

The first couple of posts will be on different types of chemotherapy, as many people I talk to don’t realise that there are lots of different types that have different ways of killing cancer cells and other effects like activating the immune system. This weeks post is all about Cyclophosphamide which is the major chemotherapy I am using in my PhD Project.

What is cyclophosphamide?

Cyclophosphamide is a type of chemotherapy and is used to treat lymphoma, leukaemia, lung cancer, breast cancer, neuroblastoma (brain cancer) and sarcoma – though in many cases it is used to treat numerous other cancers as second or third line treatments. Cyclophosphamide is also unique in that it has another use ; to suppress the immune system. It is given to patients with an autoimmune disease or to patients after transplants when it is essential for the immune system to be suppressed so the donor organ is not rejected.

I’m going to focus on cyclophosphamide as a chemotherapy to cure cancer, as this is what I am looking at for my PhD project.

How does it work?

One of the foundations of chemotherapy is that most of the drugs target rapidly dividing cells, as that is when their DNA is most vulnerable as it is being exposed for it to be replicated (of course it is more complex then this). One of the ‘Hallmarks of Cancer‘ (one of the most ‘famous’ cancer papers around described the multiple characteristics of a cancer) is that the cells continually divide, far more then most normal cells. This means that chemotherapy ‘selectively’ target cancer cells, though other rapidly dividing cells like the lining of the intestines and the bone marrow are caught up in the crossfire.

Image result for hallmarks of cancer
The ‘original’ Hallmarks of Cancer. Some more were added years after the first publication, but I will keep it simple in this blog post. 

Cyclophosphamide is an ‘alkylating agent’ which is a class of chemotherapy. It attaches an alkyl group to the DNA which damages it. As well as proliferating more then normal cells, cancer cells also have fewer ways to correct any DNA damage or errors. When a cell detects DNA damage it triggers cell death, which can be controlled and regulated (called apoptosis) or unregulated. So all in all, cyclophosphamide adds an additional chemical group to DNA which damages it, causing the cancer cell to die. There is a pretty amazing story about how this class of drug was discovered that I will feature in a future blog post!

Image result for alkylating agent
Alkylating agents add on an Alkyl group which causes the DNA strands to link together and makes replication hard, leading to the cessation of cell division and cell death. 

Another thing about cyclophosphamide is that it is inactive until it is processed by the body, specifically the liver. This means that I cannot use the actual drug in any in vitro (outside of a living organism), instead I have to use one of its active forms. I haven’t had to do any in vitro experiments so far, but when I do I’ll face this problem.

Immune Effects of Cyclophosphamide

As a cancer immunologist, I have to talk about the immune effects of this chemotherapy! One of the major side effects is lymphopenia, which is a decrease in white blood cells. This is very commonly described in the literature (I also see it in my experiments too!) but it is not necessarily bad.

One important observation was that repetitive low dose cyclophopshamide can deplete T Regulatory cells (Tregs). Why is this a good thing? These Tregs act to suppress other immune cells, like our cytotoxic T cells that help kill cancer cells. There are a number of papers describing that when cyclophosphamide removes  Tregs from tumour and periphery, the other immune cells are released from being suppressed and are able to have an antitumour effect (here is one that shows that the depletion of Tregs leads to the activation of tumour specific T cells). Cyclophosphamide also has a large variety of other immune effects, but the depletion of Tregs is the most well described and clinically interesting as it is seen in both mouse and human studies.

How does it relate to my work?

Now I don’t want to give too much away (waiting for some all important publications to appear before I spill all the beans..though this may be a year away) but I am looking at how cyclophosphamide works to cure cancers in murine models and if there is anything we can do to make it work better. It is primarily in vivo work, which is a good thing as I would have to find some active forms of the drug to work with for any in vitro experiments.


This is the end of my Pharmacy Phriday post! I could have gone into more detail but i’m going to try to keep these features simple. Don’t hesitate to ask me any questions in the comments or share with me anything else you find interesting. 

How I Compare Myself to Other PhD Students

I see this quite often in the science community (mainly on Instagram). How often do you as a student (or a Post Doc in a broader sense) compare yourself to others and is this a bad thing? I’m going to talk from my own experiences here and I would love to hear yours in the comments below. So here are some of the ways I compare myself to other students and the impact this has on me.

  • How many hours I work.

This is probably the most common way students compare themselves to others and probably one of the things that causes the most stress. I am a night owl and I often have trouble sleeping, so I tend to sleep in a bit in the morning, so I normally get into the office between 9am and 10am- which in all honesty isn’t that late. I still feel judged by my fellow PhD Students and other lab staff when I get in that late which makes me feel like i am slacking off.

 I also hate being at work and not getting any work done. You know those times where you sit at your desk doing nothing no matter how much you try. I normally end up playing on my phone instead of reading the stack of papers I need to get through or analsing data. When I feel that I am becoming unproductive I normally like to call it a day and head home. Sometimes this this is around 3pm or 4pm. I figure that instead of wasting time at work doing absolutely nothing, it would be better for me to head home and catch up on chores or have a bit of fun time. Again I feel so judged by my peers when I leave this early and I then when I get home I feel the guilt for not getting any work done and slacking off, yet again. I also like to head to cafes or the library once every couple of weeks (I am actually in a cafe now when I am writing this) to have a change of scenery while I am writing up results or analysing data but as i’m not in the lab building, I feel like everyone else is judging me.

The thing is, I know that this is such a negative way of thinking and that I should not worry too much. Everyone has their productive times and ways of getting through the stresses of a PhD. Mine is enjoying the odd sleep in or taking that break when I know nothing is being accomplished.

What I also have to remember is that I often do quite a few hours on the weekend too that most of the others in my lab don’t know as they are often not in on the weekend. As I always have mice or cells to check, I have to come in the majority of Saturdays and Sundays during the year. When I am in the lab on those day I like to make the most of it as it is a 1 hour trip each way, so I end up doing between 3-6 hours on a Saturday and Sunday as well. Even though I do end up ‘catching up’ on the couple of hours I miss during the week by sleeping in or leaving work early, I still feel guilty when my peers call me out for getting in a little late or leaving early even though I know that I am putting the work in.

  • How many papers and ‘good’ results I get.

Even though worrying about how many papers you have and the impact/quality of your results is a guarantee in a PhD, I can’t help but compare my project to the others in my lab. I always get worried that my results don’t mean as much as others or I won’t end up with as many papers as others. That I am not doing enough experiments and at the end I will have no chance of a good Post Doc while the others will have so many high impact articles.

  • How I do things in the lab and my protocols.

The last thing is very much ‘impostor’ syndrome in the lab. Whenever I am doing cell culture or flow staining I always worry that when others look at what I am doing I will be doing it all wrong and I shouldn’t be doing a PhD as the way I do my experiments is so inexperienced and ‘wrong.’ I went straight from honours into my PhD (so I came in with only 1 year of research and lab experience) and I was also the youngest in my lab for two years (I was even younger then last years honours students too!) I feel sometimes because of how young I am and that I have less experience at somethings that everyone is looking at me like ‘what the hell is she doing?’ ‘That is not how you should be doing your staining.’


I hope this post shed some light on some of the ways I compare myself to other PhD students and maybe you can relate to some of these as well. I am so interested to hear if you relate to any of these or if you have worked through these insecurities. Please let me know in the comments your experiences!

Saturday 21st July 2018- Day in the Lab #1

Hey everyone!

So I have been meaning to do this for a while, but some days I am either so busy that I don’t have time to track and document what I am doing. Other days I am sitting at my desk looking at data or reading, with the occasional trip into the lab to check cells.

But on a rainy Saturday in July I needed to head into the lab and I decided to do some flow cytometry panel optimisation, and what better time to write my first ‘Day in the Lab’ post!


So I left home just after 12pm, I was planning on leaving earlier but it started pouring down with rain at 11pm so I stayed in bed with the cats a bit longer. I also went shopping as I pass through the city on my way to the lab. I needed some new boots as my well loved pair was falling to pieces. I didn’t end up getting a replacement for them, but some other things I was looking for. I just didn’t expect to have spent nearly two hours shopping, so I didn’t get to work until 2:30pm.

Once I had gotten to the lab and collected my blood samples from my subjects, I started plating them and started my calculations. I had 15 minutes to wait for my red blood cells to lyse, so I made up all my antibodies so they were ready to go. I have been having a couple of problems with my 7 colour flow panel to look at T cells, B cells and NK cells in blood. I was hoping that by titrating some of my antibodies this problem would be fixed! At just before 4pm I was ready to add on my antibodies for my first 20 minute incubation.

I did some Lab book arts and craft while I had the incubation, and then it was back into the lab to wash my cells. I normally have to spin them in the centrifuge for 3 minutes 3 times, and it may not sound like much but it does end up being time consuming. I then had to permeabilise my cells (so I could stain for an intracellular marker, FoxP3) which is another 15 minute incubation!

I put on my second antibody stain at around 5:40 which meant I had 20 minutes to go grab something to eat as I was starving! Luckily there is a burger place down the road which makes amazing burgers and their chips are one of the best I have ever tried. I couldn’t take my time to savour it though as soon as I got back to the lab, my timer went off and I had to wash my cells again and get them ready to run on the cytometer. I was able to eat my dinner after all of that, before I headed down to sit in the cytometry lab for an hour and a half. At 6:30pm they cytometer was turned on, fluidics started and HTS primed. The end was near.

I had an article to read for Journal Club, so once the setup was all done I was able to start reading it in preparation for my presentation on Tuesday in front of the lab. After my samples had run, I had a quick look at the data (my NK cell staining didn’t improve at all!) which turned out to not have really fixed anything. That is the essence of science though! I was out the door at 8:21pm ready to catch the 8:32pm bus and begin my hour journey home.


I had a lot of fun writing this and taking photos as I went through my day. It is interesting to see where the time goes as it feels like time flies when I am in the lab and working on my research. Let me know if you liked this type of post as I am keen to do it again in the future, every two weeks!

 

The trials and tribulations of supervising an Undergrad Student

Was I as inexperienced in the lab, shy and demanding in the lab back when I was an honours student? When I go back and read some of my writing from way back then (and by way back I mean 2016) I cannot believe how much I didn’t know and compare that to how much I know now. The answer the above question is yes, I had no clue what I was doing in my first year of research!

I mention this as this year I was given the opportunity to supervise an Undergraduate Honours Student for their project and they would work alongside me as I work on my PhD project. As I want to continue on in academia, supervising students is such a vital part of science and I couldn’t say no to the experience and opportunity. It doesn’t hurt that it also looks good on your CV.

We just passed halfway through the year and are over halfway through their project and I have to admit, I had no idea how much work it would be!

Instead of my usual paragraphs, I decided to summarise my experience in a series of dot points that detail the ‘Trials and Tribulations of Supervising a Student’.

  • They need supervision for most of the experiments during the first half of the year. When you come into Honours you have some laboratory experience, but not much. By the end of honours the students should be able to work independently and understand the protocols and concepts. But to get there require a lot of guiding through basic lab techniques and checking over their shoulders to make sure things are going smoothly. For some work (like with animals or very important samples) I’ll still take the lead and watch them like a hawk as any mistakes would set me back weeks and we always have to watch the budget.
  • They don’t have the knowledge and experience to adjust protocols, troubleshoot or fix mistakes. No one did when they started in the lab! I get inundated with simple questions that I think are very easily answered and common sense, but they just don’t have the understanding to work it out themselves. It really makes me think about how much I have learnt over the last two and a half years I have been in research.
  • You have to let go of control of your experiments. I am a massive control freak and I like things done a specific way, especially when it is anything to do with my experiments. When you have a student you have to let them be independent and work by themselves, as by making mistakes they will learn a whole lot faster. I have to let go and accept that things won’t be don’t exactly how I like, experimental groups might be mixed up and the protocol might be followed wrong. Though, I try to strategise as to what experiments I don’t mind them making a mistake with.
  • You can delegate some experiments you don’t want to do or are time intensive. Don’t look at me like this, my very own supervisor suggested this! As they are in the lab to get experience (and as a PhD student there is never enough hours in the day) students are great at performing the above type of experiments. MTT assays include a whole lot of techniques like cell culture, dilutions and accurate pipetting. For my project we needed lots of replicated for multiple cell types, and what better way to get a lot of experience at basic skills then for an Honours Student to do it. By the end, they were a gun!
  • At the end, you can look back at how far you both have come, and feel good that you have helped train and inspire a future scientist. Because at the end of the hard work, you have to be positive and see the result of your hard work! You were once an Honours or an Undergrad at some time in your science career!

Have you had any experience supervising a students or was your own experience as a student positive! Let me know in the comments!

Who is the Scientist and Her Cats?- An Introduction to my Blog

These introduction posts are always so hard to write and honestly, who ever looks back at them in a couple months time to see where it all started? None the less, I would feel weird starting this blog without fulfilling this obligation of giving an introduction of who I am, what I do and what this blog will be about.

So, my name is Caitlin and I am currently in my second year of my PhD in Australia. I’m working in the cancer immunology and biology field and I love my work. Seriously, I love what I do. I get excited starting experiments, thinking of new ideas and what I can do next, waiting for some new results and ticking things off my massive to do list (I started a whole new system and i’m excited to share this on my blog in the coming weeks.) I love research and aim to move into academia once I finish and get those all important three letters after my name.

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The filter is to hide the exhaustion of being in the lab for 6 hours on the weekend.

I also do other things apart from research (though at the moment research and lab work is turning into both a job and a hobby.). I play sports and go to the gym when i’m not in the lab until 7pm at night. I knit, sew and play video games. I love esports and true crime documentaries. I also love books and run a book blog as well (which you can fine here!)

I also have two wonderful cats, Bucky and Schrodinger who are a very important part of my life. My wardrobe also includes a number of cat themed clothes which I wear shamelessly.

But onto the big question…

WHAT IS THIS BLOG ABOUT?

I’ve always liked blogging but never found a way to intergrate it into my life or have a clear direction to head into (apart from my book blog which keeps ticking on). I’d start a blog, write a couple posts and then lose interested.

I discovered the science communication and general research community on Instagram and enjoyed seeing other peoples experiences in research and in the lab. Explaining to people what your research is all about and introducing people to how research works and what being a scientist actually entails is something I am passionate about and I always talk to my friends (who are mostly non-scientists) about what my project is and give them updates.

Because I am always so long winded in my writing, I thought i’d summarise what i’ll be putting on this blog in dot points. My supervisors always tell me to be more succinct, but I just love waffling on!

  • My experiences as a PhD Student. It’s such a unique experience for everyone and I’m excited to share all my success, failures and how it all progresses up to the point I am finally a Doctor,
  • Tips and Advice for Research Students. Everyone comes across things during their PhD that they wish others knew, or worked out the hard way.
  • Relationships and Dating. I just feel like writing about this. Why you ask? Because being a scientist and trying to have normal relationships is hard to balance with the 50-60 hour work weeks. I’m also a complete newbie and people might find my experiences either relatable or make their day a bit brighter.
  • Food and Exercise. I love cooking and have just started making lunches and trying out new things, so if one of my experiments in the kitchen works out, i’ll share it with you all!
  • Travelling…to Conferences. I have not yet attended a conference outside the state, but i’m looking forward to being able to see the world, visit some other labs and cross off some countries on my list.

I’m always open for writing about anything else! Whether it is a technique I am using in the lab, book recommendations (I have got plenty!) just let me know in the comments and i’ll give it a go.

That is all from me at the moment. I’ll try to post 2-3 times a week…unless the lab work gets so hectic all I do is pipette and sleep!