Time done: 30 months
Time left in lab: 9 months
Time to write up: 9 months
Mood: wildly bouncing from euphoria to depression

So I thought I would do a quick update on how my PhD is going since it’s been a while.

I am officially ok with my hypothesis!

Before Christmas was the hardest my whole PhD has been. I had spent a year analysing and testing my Illumina MethylationEPIC array (which looks at over 850,000 CpG sites across the genome - not that many considering how many there actually are). I found sites that had significant increases and decreases in methylation when I treat with my drug, spent months validating them using pyrosequencing and what did I find? Nothing. It didn’t validate. It was soul crushing.

Buuuut I bounced back. Had a massive rethink with James (my supervisor). We thought about what my drug theoretically does and how that could affect epigenetics and I came up with a new, testable hypothesis. We were assuming my drug does a very specific thing that can be reproduced over and over (eg it always causes the same change in DNA methylation in the same place regardless of what cell line I use or how many times I test it). But maybe it’s not so specific but a bit more random, which is totally fine!

This new direction also means my Illumina MethylationEPIC array analysis wasn’t a waste of time. Celebrations all around!

And it seems to be going well so far. Well except that I have been troubleshooting the same western blot for nearly three months (and beating my head against a wall. Chairs may have nearly been flung through windows). There has been some tears not gonna lie. It’s hard to do the same 2-4 day experiment over and over to prove the result you got in the first place (in bloody January) was correct all along. Science - when you know you’re right but you have to show all the wrong ways to do it to prove you’re right!

So what’s the plan now?
Well I am going to the American Association for Cancer Research (AACR) Conference 2018 Chicago in April (there will be many vlogs, blogs etc) to present what I’ve found so far! Absolutely terrifying since I’ve only started to believe in my results like....last week.

I have about 9 months left of work in the lab before I need to write it all as a thesis. That will consist of learning a few new techniques (RNA-seq, ChIP-PCR) and to get a bit more of an idea of what’s going on and how I can sum this all up in a pretty bow.

I’m also getting another masters student to supervise (YAY) which I’m very excited about because I really like the project I wrote and the results regardless of what comes out are gonna be very interesting. She’s starting at the start of May and finishing up in September.

I need to write some papers! I apparently have to publish my data (who knew) so the next six months will be writing up what I've done so far in a paper, getting it peer reviewed by people in my group so I can find any holes and plug them before December. I can then sent the actual papers off for real peer review and (hopefully) publication. 

And that's it. Sounds simple enough but it's taken 7.30am starts working 5-7 days a week to sum up everything I've done since August in a few paragraphs. I've even started drinking coffee in work. I shake violently when I drink coffee. It's not a good idea.

I have one last thing to say to anyone thinking of doing a PhD, to people currently doing PhDs or anyone living with a person doing a PhD: 

To the person thinking of doing a PhD: be prepared. I want to scream at you "DON'T DO IT, IT'LL RUIN YOUR LIFE" but I won't. We need more researchers so we need more PhDs. But I will say be prepared. It is not all rainbows and unicorns. It's hard and it will drain the soul out of you. But then you'll get a result and feel like the smartest person in the world. You will love and hate the 3-4 years of your life doing a PhD. But really...be prepared to hate it a lot more of that time than you think. 

To the person currently doing their PhD: you are a god damn hero. Keep going. You may feel like you're drowning or that "maybe a masters for this isn't so bad, I should give up". DON'T. You have given your blood, sweat and tears to this thing. You are going to finish. Even if I have to carry you. But seriously. You have got this. You are smarter than you know, you are incredibly dedicated and you will finish. No one knows what doing a PhD feels like until they have done one. No ones knows the soul crushing pain. I know. And I know you have got this. 

To the person living with a PhD: please be patient. I know you don't understand what they're doing. I know you don't get why a little comma could cause a massive mental breakdown, the consumption of ALL of the ice cream and you getting shouted at but trust me there's a reason. It's hours, weeks, months or years worth of work that your loved one has just watched go down the drain (this specific example is for programmers but is applicable to all types of PhD). Just keep supporting and loving and caring for the lunatic PhD because they need it. And thank you for being there. Your presence means more than you will ever know. 

​
PS: I know I haven't been posting a lot. I do apologise but every second of my waking life is going into completing my AACR poster so bear with me. 

PPS: Apparently I have a very neat desk in my office and all other desks should aspire to look like mine......Weird email sent around the office!? So.....don't get too jealous everyone...

Cute animal photos keeping me sane are courtesy of the wonderful Fota Wildlife Park Ranger (Liam) supporting this lunatic PhD (me). 

This is going to be a long and technical one sorry. 

This month I want to talk about an experiment I've done pretty much every day for the last three months (plus continuously over the last 2.5 years) - Western Blot. 

Western blots are used to visualise and identify individual proteins. In this technique you have a solution (called a lysate) filled with the majority of proteins from cells. This technique separates these proteins out by size and allows you to stain for specific proteins you want (more on this later). This is the standard way to visualise proteins but it is very subjective and is tricky to perfect (I hope you will appreciate why after reading this). 

The proteins are visualised by staining them with antibodies specific to that protein and then using a chemical reaction to produce light which can be picked up by a machine. The resulting image is of black bands. The intensity of the black band determines the approximate level of protein present. 

There are a few steps to Western Blotting which I will go through. The whole technique can take 1-3 days depending on what proteins you are looking for and what you choose to do in each step. 

Steps to Western Blotting:

1. Gel preparation, protein preparation and buffer preparation
2. Loading gel and running SDS-PAGE gel electrophoresis 
3. Transferring proteins onto membrane
4. Blocking non-specific binding
5. Antibody staining of proteins
   1. Primary antibody incubation and washing
   2. Secondary antibody incubation and washing
6. Developing 

A little bit of terminology before we begin:

• Blot: a blot is what we call the membrane once protein has been transferred to it (more later). A blot can be the whole gel you ran in electrophoresis or part of that gel. 
• 1°Ab: primary antibody 
• 2°Ab: secondary antibody 
• Loading control: to make sure that you have loaded the same amount of protein in each well and to ensure that any changes in protein abundance in response to say a drug is real you also stain for a loading control. This is typically an abundant protein found in every cell. Usually beta actin or tubulin are used. 

STEP 1: Preparation

Reagents and Buffers
Before you begin a western you need to make sure you have all your reagents prepared. I will NOT be going through this, all I will say is you need reagents for

• making your gel
• making up your protein that you will load onto the gel (loading buffer)
• the buffer the SDS-PAGE gel electrophoresis will run in (running buffer)
• the TBST you will use to wash your blots (wash buffer)​

Protein Preparation:

When you extract your protein from your cells you end up with a protein lysate. This contains the majority of the proteins in your cells. You don't know what the concentration of the total protein is but you are sure that each sample doesn't contain the same concentration. This is due to how well the extraction went in each individual sample but also how many cells there is to extract protein from. There are a few ways of finding out the concentration of your protein which I won't go through (I use the Bradford Assay from BioRad). 

What you do need to know is that for each sample you need to make up a solution of protein, water and loading buffer to load onto your gel. You can use as much or as little protein as you want, I typically use 10-15ug per well. I load 20ul per well so I need:

• Protein - e.g. 5ul
• Water - e.g. 10ul
• Loading buffer - ALWAYS 5ul per well 

​There are many types of loading buffer, I use Laemmli buffer.
The loading buffer has a couple of functions. You are using an electric current to make the proteins travel through the gel. Proteins are all different charges so the buffer makes sure all the proteins have the same charge (negative) - this is done by a chemical called SDS. Proteins are globular structures. These don't run though a gel very well so you need to unravel the proteins into single strands (called denaturation).  The buffer will start this process - a chemical called β-mercaptoethanol breaks disulphide bonds. The loading buffer also has a dye in it. This is called the "loading front" which runs faster than your proteins. This allows you to track how far your proteins have travelled through the gel (image later). ​

A quick note - usually the protein samples you have prepared will be blue once you add the loading buffer and boil it. This is because the dye in the loading buffer is blue. However, the protein I will show in this post will be yellow. This is because I extracted the proteins using acid and the acid in the lysate turns the buffer yellow. Once the gel starts running the dye front goes back to blue.

Gels are made up of:

• 30% Acryl-bisacrylamide mix - polymerizes to form a matrix, which allows proteins to pass through
• 1.5M Tris (pH 8.8 or pH 6.8) – allows a negative charge to be applied to proteins
• 20% SDS - denatures secondary and tertiary protein structures and adds a negative charge. 
• 10% ammonium persulfate – an oxidising agent often used with TEMED to catalyse polymerisation of acrylamide (Added just before setting gel)
• TEMED - stabilises free radicals produced by APS and improves polymerisation (Added just before setting gel)

The acrylamide will set into a gel which has pores in it. The protein will travel through these pores. The percentage of acrylamide used determines how big these pores are. Large proteins run slowly through a gel whereas smaller proteins will run very quickly through the gel. A lower percentage gel (e.g. 7%) will have large pores, allowing larger proteins to run faster through the gel. However you are likely to lose all the smallest proteins. A higher percentage gel (e.g. 12.5%) will have very small pores which slow down the small proteins, allowing you to visualise them easier. However all your largest proteins might not run as they can't past through the pores. 

There are two types of gels used in gel electrophoresis - a stacking gel and a resolving gel. They're pretty much made up of the same ingredients (a stacking gel is slightly more acidic pH 6.8). 

• The stacking gel: is usually a very low percentage gel (4-5%), meaning it has very big pores. This is where the comb is added to form wells which allow you to load your protein into the gel. The stacking gel allows all the protein to line up, like sprinters on a start line, so the proteins run smoothly and evenly through the gel. 
• The resolving gel: this is where your proteins separate by size (resolving). The percentage of this gel depends on the proteins you are looking at. 

Steps to making a gel:

1. Make up your cassette in the stand
2. Add the resolving gel FIRST and allow to set. Typically you put a little isopropanol on the top (which won't mix with the resolving gel) to prevent evaporation while the gel is setting
3. Remove the isopropanol and wash with water 
4. Add the stacking gel 
5. Place in a comb into the stacking gel. This creates the wells for loading protein. The number of wells depends on the comb you use - typically 10-15 wells. 
6. Allow to set

I have made up a 12.5% gel for this example to run histone proteins which are approx 15-17kDa in size. I will also stain for a loading control, beta actin, which is 45kDa in size. 

STEP 2: Loading and running SDS-PAGE Gel Electrophoresis

The next step is to load your prepared protein into the wells in your stacking gel and running an electric current through the gel to allow the proteins to travel from negative to positive. 
​
The gel(s) are clamped into an electrode chamber and placed in a running tank. The centre is filled with running buffer. The running buffer allows an efficient flow of electrical current to pass through the gels. It also prevents the gels from drying out which you do not want. 

STEP 3: Transferring proteins from gel to PVDF membrane

Once the gel has run enough you can stop it. This depends on how long you want to wait for and what proteins you're looking for. My proteins are very small (17kDa) so I can stop my gel once I see the 17kDa ladder band is far enough from the loading front. 

The next step is to transfer the proteins from the gel onto a membrane. You cannot stain for your proteins on the gel as it is far to delicate and not permeable - the protein only runs through the gel because we created the wells. The membrane is more permeable and allows you to stain for proteins. 

There are a couple of (messy and time consuming) ways to transfer proteins but I prefer to use the iBlot dry technique. This basically transfers the proteins using a machine in 5 minutes (compared to 1-2 hours). The transfer stack consists of:

1. bottom part: which has the membrane (in this case a PVDF membrane)
2. middle part: the gels, covered in a piece of damp filter paper
3. top part: allows electricity to be conducted
4. sponge

Again an electric current is used to push the proteins through the gel into the membrane. However the voltage is very low. As we know, small proteins move very quickly. The low voltage prevents the small proteins from passing straight through the membrane. 

So how does it work:

1. You remove the gel cassette(s) from the tank
2. You gently open the cassette. You cut off the stacking gel and the loading dye front. The gel is placed in water until ready to transfer to prevent it from drying out
3. The bottom stack is opened and the gel(s) are placed on top
4. A piece of filter paper is quickly wetted and placed on top of the gel(s)
5. A roller is used to gently remove any air bubbles and excess water
6. The top stack is placed on the filter paper (metal side up)
7. The whole completed stack is placed in the iBlot machine, with a sponge placed in the lid
8. The lid is closed firmly, ensuring there is a complete current
9. The transfer is run at 20V for 5 minutes

After the transfer is complete you need to be VERY fast. You have to quickly remove the stack from the machine, get the membrane out of the stack and place it in TBST. The membrane CANNOT dry out or else all is lost. You can check your transfer at this stage using Ponceau red, which is a red dye that shows up all the wells and bands of proteins but I did not do that today. 

STEP 4: Blocking

The next step is to block any unspecific binding. The antibodies are usually polyclonal - meaning they can bind to other proteins that aren't your protein of interest. To prevent this and also to get a nice clean image at the end, you block unspecific binding. 

You can block using either of these two reagents:

1. 5% BSA/TBST/NaN3
2. 5% Milk/TBST

The reagent you are using depends on the antibodies and proteins you are looking for. I block in 5% BSA/TBST/NaN3.

Before I block I cut my membrane so that I have the two individual gels again. You don't have to do this but I like to. At this point I just cut the excess off using the ladders as a guide. I then mark with a pen on the ladder what gel it is. 

The membranes are blocked for 1 hour at room temperature on a rocker. 

This is now when we can call out membrane a blot. 

After blocking you can cut your blots to stain for multiple proteins. In this case I cut at 36kDa band (blue band above the bottom red band on the ladder) to stain for my histone proteins and also my beta actin loading control. 

STEP 5: Antibody Staining of Proteins

This technique as I said uses antibodies which bind to specific proteins and you can them visualise these antibodies using a chemical reaction. 

​ The figure below gives a rough idea of how the technique works. 

1. a primary antibody semi-specific to the protein of interest binds to a particular part of the protein.
2. a second antibody with a HRP (horse radish peroxidase) attached to it binds to the first antibody. 
3. A peroxide solution is added which reacts with the HRP. This chemical reaction produces light which is detected using chemiluminescence. NOTE: the luminol enhancer solution is added to increase the efficiency of the chemical reaction making it easier to see. 

The antibodies are created in different animal models (please don't ask how cause I have no idea). So if your primary antibody is developed in a rabbit then the secondary antibody will be goat anti-rabbit (i.e an antibody developed in a goat to bind specifically to rabbit-developed antibodies). There are some human antibodies but they're incredibly expensive. 

The primary antibodies are made up in the buffer recommended by the manufacturer usually 5% BSA/TBST/NaN3. The recommended concentration is usually given by the manufacturer - typically 1:1000 or 1:2000 (i.e. 1ul antibody in 1ml solvent).  
The secondary antibodies are made up in usually either 5% BSA/TBST or 5% Milk/TBST. The BSA doesn't contain NaN3 in the secondary because sodium azide (NaN3) inhibits the secondary antibody. The concentration of the secondary depends on how abundant the protein is and how long you develop it for. For example beta actin, which makes up part of the cytoskeleton of your cells, is an incredibly abundant protein so the secondary concentration is 1:50,000 BUT another protein I look at p-AMPK is not so abundant and the secondary concentration could be as low as 1:1000. 

NOTE: for beta actin, you do a 1 hour incubation at room temperature

STEP 6: Developing

The final step (thank god) is to develop your blot. This step adds the peroxide and luminol enhancer solutions (collectively known as ECL solutions) to the membranes. You then take the membranes to a chemiluminescence machine which will detect the light emitted and give you an image in return. 

Steps:

1. an equal amount of peroxide solution and luminol enhancer solution are added together. 
2. The blot(s) are dried slightly on tissue and placed in the ECL solutions
3. The blot(s) are incubated for 1 minute in the ECL solutions 
4. The Blot(s) are transferred to a clear plastic sheet and covered with another clear plastic sheet
5. Excess bubbles are removed
6. The blot(s) are placed in the chemiluminescence machine and developed for maximum 15 minutes. This can be done in increments (e.g. 1 minute increments for 10 minutes) ​

You end up with a picture which has black bands. As I said at the start the intensity of the bands indicates how much protein is present - very dark means a lot, very light means very little and nothing means nothing. ​

The image above shows the loading control (beta actin) for a blot I have done for two cell lines, MCF10A (lane 1-3) and MCF12A (lane 4-6). The bands are very dark indicating that the protein is very abundant. What's important is the bands are almost the exact same size and intensity as each other (different in the two cell lines) indicating that my loading was very even (wahey).