Student bloggers

Life as a student in Bath

Topic: Maho

Learning and collaborations

📥  Faculty of Science, Maho, Postgraduate

Recently, I got a chance to learn about a technique which I knew about but have never used before. This was definitely a great experience for me, as a big part of doing a PhD is learning new techniques and expanding your knowledge. There are certain techniques and experiments which will be applicable for a lot of fields, while others are more specific to certain fields, and having a chance to use a technique which may not necessarily be a standard in your field is rewarding and also helpful in improving your knowledge (as you can probably imagine). Also, it's like a breath of fresh air when you are stuck repeating the same experiments.

Projects will require a different set of techniques, and each set will be different. And the truth is, there is a difference between knowing the theory behind the techniques and knowing how to use them (however, knowing the theory definitely helps, especially when you’re stuck); even though I knew the theory of Western blotting, it still took me ages to get one to work! Sometimes, when you need to do a particular experiment that you've never done before, this can mean collaborating with other people in your group, or other groups. Given the vast amount of techniques available, you end up knowing quite a lot about a few, selected techniques, so collaborating is a fantastic way of learning that little bit about a different technique - who knows, that little bit of knowledge may in fact give you an edge in future job applications! I guess that is also why a lot of research papers contain a lot of authors.

This PhD has been enlightening in that I have got to see how research actually works in reality; from how to figure out why the experiment is not working, to getting an insight into how long it actually takes behind the scenes – I now know how long it can take to get the data for a paper, then how long it takes after that before the paper is actually published, and I really didn't anticipate how frustrating that all can get at times. All in all, I have really enjoyed getting to use the techniques which I have learned, and I suppose learning something new recently reminded me of the thrill of research and why I wanted to do a PhD in the first place; definitely helpful to be reminded of that when you are lacking motivation... Use opportunities to expand your knowledge when you can, because, like I mentioned above, you never know when that little knowledge may come in handy...

 

Thesis...

📥  Faculty of Science, Maho, Postgraduate

So, I guess most of you will know that you have to write and submit a thesis to get a PhD. It’s basically a book on your research, detailing what experiments you did and why, what you found, etc. Now, as you may have gathered from reading my blogs (thank-you!), I’m coming towards the end of my PhD, meaning I’m now starting to write this book... well, at least trying to anyway! It’s something that’s been in the back of my mind since I started, and now it’s time to start tackling it, it’s really scary! – I’ve never written anything that long, so it just seems daunting right now.

Some people will stop doing lab work and concentrate on writing full time – I’m not currently doing that, as I have not finished my projects yet. Now, I originally thought that writing while still doing lab work would be... well, not easy, but... do-able; it’s actually proving trickier than I anticipated. The difficulty is that lab work obviously takes time out of your day, so even if you start writing and get into a good flow, you may need to disrupt that to get back to lab work, which then makes it hard for you to get back to writing. Or, you may only have a short gap between stages of experiments, which makes it difficult to get started. How do you find the motivation in those scenarios?

Another thing that has an impact on me is the fact that my projects are still not complete, therefore what can I write about? Is there any point in starting something that may change anyway? – knowing what research is like, what you think will happen may not actually happen at all! Also, if you are aiming to get your research published, should you be concentrating on writing your thesis or the paper? – I personally say concentrate on the paper, as that will be an important factor when applying for jobs, and also when you come to do your viva (so I’ve heard). You can then modify the paper for your thesis – win-win really! Or put the papers together as a thesis, which I believe is now possible in my department.

One saving grace has been being around post-doc.s; it’s so helpful to hear about how they approached their thesis. Most have said something along the line of “start with your materials and methods/introduction”, and that’s the approach that I’ve taken. And I have to say that it’s great to know that I won’t have to sit down and write a whole materials and methods section from scratch! Of course, your supervisor/other academics will be able to advice you too; interestingly, I’ve had one piece of advice that it’d be better to concentrate on finishing lab work, and writing full time after; now, I can see advantages to that, as you probably gathered from above. However, due to the fact that my project is not finished, I’m currently concentrating on lab work. Who knows, I may finish lab work at some point in the spring, maybe I won’t...

How you approach writing a big “report” like a thesis varies from person to person; I guess the trick is finding what works for you. My advice for those about to embark on something similar, like your thesis or a final year dissertation, would be to start with the introduction and materials and methods, like I was advised. That has definitely worked for me, and that can be started even before you have a definite idea of what the outcome of your project is. Another thing I find helpful (and what I should start doing more often!) is finding somewhere to go and write; library, café, doesn’t matter. It’s better to be away from the office/home with the intention of writing, and I’ve recently discovered the graduate commons areas in 10W (4th and 5th floors); I went there with my laptop and a pair of noise-cancelling headphones, as I find background noise distracting and music helps me concentrate better, and was more productive writing there than in the office. If you are still in the lab like I am, just find a couple of hours where you are not doing anything in the lab, go somewhere else and start writing.

Now, do I have a gap tomorrow...?

 

Publishing

📥  Faculty of Science, Maho, Postgraduate

Publishing scientific papers is key for career progression, and it’s not until you start thinking about what should go into a paper that you realise how much work goes into one – for example, it’s taken me most of my PhD to get the research done to even start writing the paper. Then it was time for the manuscript to go to our collaborators, and I’m now (still) doing more experiments. And really, that’s only half of the story; once it’s ready, then it may or may not be sent out to reviewers, who might say more experiments need to be done!

The main factor in getting your research ready for publishing is getting the experiments done, and, as I have mentioned in previous blogs, they don’t always work the first time you try it. This then takes time to try to trouble shoot, which means that another month, two months, go by. It’s scary really, how time flies sometimes! You may also be asked to do experiment(s) for other people’s research – I’ve had the opportunity to do this, and it’s nice to know that I’ve been part of different research projects. I enjoy learning about what other research goes on, and it has been great that I’ve been able to be part of projects outside my own.

Once the manuscript is ready to be published, it gets sent to journals – now, I don’t really know too much about journals and their impact factors (rankings, basically), I can’t say much about this – where it either gets sent out to reviewers, or rejected. The reviewers then make suggestions for improvement, or rejects it. Now, this could mean more experiments, and that again could take a month or too! So all in all, you can see how quickly time flies in this process. Next time you find yourself reading a research paper, bear in mind that it probably represents years of work, possibly by a big group of people.

 

Choices…

📥  Faculty of Science, Maho, Postgraduate

Life is full of decisions we need to make, and sometimes that’s not easy. Right now, being in the latter stages of my PhD, the big decisions I need to make is “what next?”. “What are my options?”. “What do I want in my career?”

Sometimes, it does feel like I’ve ended up here without really thinking about the next step – I mean, I never really imagined that I’d be doing a PhD at all! For me, it was more a case of “I liked doing my dissertation project, perhaps I would like doing something similar”, and I have no regrets. But, when it comes to thinking about my career, rather than more short-term goals, it frankly scares me… Am I meant to know what I want to be doing in, say, 10 years’ time? I think part of the reason I get scared is that I feel as if my decision needs to be a concrete one, which, thinking about it, doesn’t really have to be… right?

It wasn’t until recently, when I attended a PG Skills course on careers, that I realised I basically had most of what I thought was important in my career already. That seems something totally unexpected if I’m honest! Well, perhaps deep down I knew, but that really was eye opening! Although I’m not yet decided on what my “end goal” is, I have an aim for the near future, and that’s far more than I thought I had.

Knowing now that I want to look for post-doc. jobs, it has made it slightly easier – however, there is still the question of what exactly I want to work on. For now, it probably would be ok to just look for projects that are interesting to me (which hopefully will match my skills!), but then what? Would that project guide me to the next stage? Or what if it only confuses me? – actually, is there any point in worrying about it at this stage? Is there anything wrong with waiting to see what opportunities arise, and taking them when they come along?

I think this is probably a hard choice for everyone, and there probably is no right or wrong answer in terms of how we go about making this choice – everyone will have a different way. The one thing I hope for is that, whatever I do decide, I will be happy with my choice and have no regrets.

 

The social side of a PhD

📥  Faculty of Science, Maho, Postgraduate

Being a PhD student is time consuming, but this does not have to mean that you spend all your time working. In fact, I think it’s very important to socialise with other people, as it can otherwise become very intense! Things like getting a group of people together to go to the Parade can give you the extra motivation to get things done when you’re struggling, and even things like going out of the office for lunch with a few people will give you an opportunity to step away briefly, to come back refreshed. It’s important not to get too caught up in the PhD, I think…

One thing I appreciate about being here is that there are social events for postgrad's, students and staff in our department. From September induction week, Halloween party, Christmas dinner, international food evening and the Cider and Ale festival, to something as small as Friday coffee mornings, it’s always nice to have a chance to socialise with other people in the department. These are organised by PGBio, which is basically a group of us postgrad’s in the department, and something I’ve been involved in since the beginning of my time here. Being in PGBio has given me the opportunity to “work” with people outside my lab, while also meeting others in the department – being away from the main B&B building, I don’t see many of the other fellow PhD students usually!

These events are usually open to staff too, and we do get some postdocs coming along. This is a great opportunity to get some advice! – From advice about an experiment that you’re struggling with, what you should be aiming to achieve during your PhD (such as; applying for travel grants, publishing, experiencing as many techniques as possible) to how they approached writing their thesis, and also finding out how they got to where they are. All this is very useful, especially as I’m coming towards the end of my PhD and am going to have to start thinking about what I want to do next.

So, if you are looking to do a PhD, make sure you take these opportunities to socialise - day to day, it can be a bit of a bubble, so I see these socials as great opportunities to escape the bubble! Not only that, but they can also be ideal places to get some advice from others; people from outside your lab will have different expertise, which may in fact be very useful!

 

Welcome to Another Academic Year

📥  Faculty of Science, Maho, Postgraduate

Once you get into the swing of things, days begin to merge. When summer arrives, things go quiet.

Having about three months of quiet, you quickly get used to that. Then, the next academic year starts…

New students start, others return, leading to a busy campus, packed buses and traffic jams. Having to be careful about when you leave for the bus and having difficulty finding a table for lunch…

New people starting in the lab and department, along with the project students. A scramble to try find places for them all. Helping them get their bearings, and social events to meet them…

New set of seminars in the department, and for me, an invitation to attend another. New set of practical’s looking for demonstrators - hoping to get the slots…

Time to say goodbye to some old friends, who have finished Masters and PhD. - thinking about my own thesis…

Welcome to academic year 2016-17

Hope it will be a good one for you!

 

“We need to do more for women in science”

📥  Faculty of Science, Maho, Postgraduate

This is the title of an article I found online, in the journal Science. Clearly, there are still issues in terms of bias against women in science/academia – and I’m sure this is not something that’s limited to science and academia. The article mentions incidents, and thankfully I have not experienced anything like that yet, and for the majority of my university life I have been looked after by female academics. And it is definitely good that there are schemes to support women in science, such as Athena Swan.

But here’s a thought: a study published in 2015, in which the authors used hypothetical applicant profiles for an assistant professorship in various fields, found that in most cases women were favoured over men. So if there is a higher preference to hire women, why is this not reflected in reality?

According to an article in the Guardian (citing an article in New Scientist), this may be due to the fact that early stages of a research career involves short-term contracts in various places; this coincides with the time when people want to have children, and the nature of these post-doc. contracts is hardly ideal for anyone wanting to settle down to start a family. Now, this would equally affect men as well as women, but further in the article it cites a study showing that men are more likely to have partners who are willing to stay at home to look after the kids while women are more likely to be with a fellow scientist. This would create a situation where women are more likely to have to choose between a family and their career, and it is a sad thought that capable young scientists are having to make this choice.

This got me thinking: is this choice something that women have to face regardless of what they do? Or is it more difficult in science? Surely there are men out there that will have to make this choice too? Personally, my main focus for the future has been a career. This does not mean that I don’t want to get married and have a family – is this something unrealistic for me to try and achieve?

I guess it’s hard for anyone to make these decisions. It took me a long time to think about what exactly I wanted to do, and it seems like I’ve ended up here without really thinking too much about what next! Right now, I am happy to be doing what I’m doing, and somehow it feels like I am where I’m meant to be right now… Doing this PhD has made me realise my passion for research, and although I have not really thought too much about what I will do after, my feeling is that it will involve research in some form or another!

 

My Motivation

📥  Faculty of Science, Maho, Postgraduate

One of the reasons I chose to do my PhD in microbiology is that I believe a lot of modern medicine relies on the ability to treat infections. For example, without that ability, things like surgery, transplants and immune suppression will be too risky. And the scary truth is that antibiotic resistance is becoming a big problem. Recently, a review on antimicrobial resistance by Lord O’Neill was published, and this article summarises the key findings.

A brief overview of how antibiotic resistance can occur: sometimes it only takes one change in the DNA sequence of the bacterium to become resistant to an antibiotic, and if that particular species is a fast growing one this can happen quite quickly. Another way of acquiring resistance is by picking up bits of DNA from the environment, which is not necessarily from the same species; these genes exist because antibiotics are based on products which are made by bacteria. So in a way, we’re trying to control nature by using chemicals derived from nature. While bacteria can adapt to this new challenge easily, it can take a while to adapt the chemicals. This leads to a situation where the number of antibiotic resistant infections are on the rise, but the number of agents which are available is not rising at the same rate; it was last year that a new class of antibiotic was found after almost 30 years.

So what can be done to make sure that we keep antibiotics effective? Certainly more awareness and control of its use will be helpful (especially in veterinary medicine), as will improving hygiene and surveillance – points which the report highlighted. But I believe focus on research and development is important, not only to discover new antibiotics but also to create new tests to ensure that appropriate antibiotics are given – again, highlighted in the report.

While these above points are important, I also believe that the pharmaceutical industry need to play a part too – after all, even if discoveries like teixobactin are made, there are lots of steps before it can become a medicine and I believe that this will be difficult without the involvement of pharmaceutical companies. Now, the fact that resistance to antibiotics can occur rapidly means that it can become ineffective very fast – not great if you are trying to cover the cost of its production! There have been proposals both from the pharmaceutical industry and in the report of finding alternative ways to fund antibiotic discovery; this I think will be crucial.

Funding for research I think is another crucial piece of the puzzle in terms of finding new antibiotics or new ways of treating infections – that is how teixobactin was found, and I hope that research like this will be happening long into the future. As technologies improve, we are able to increase our understanding of how the infection process works, and who knows, this may lead to a change in how we approach infection treatment. With genome sequencing improving all the time, there may come a time where a clinician may be able to sequence a patient sample quickly, and then work out if antibiotics are necessary or not, and also work out which antibiotics will be effective/ineffective.

I am hopeful that with the above report and the Longitude Prize being focused on antibiotic resistance we will be able to tackle this problem which may indirectly affect a lot of us.

Reality of doing research

📥  Faculty of Science, Maho, Postgraduate

Things don’t always work. I know I've mentioned this before, but it’s the truth!

This time last year, I was in the middle of trying to get a Western blot to work. A Western blot is a technique with which you can pick out a specific protein in a mixture of proteins, and as it involves various reagents and steps, some of which can be changed, there are quite a few things to tweak. I was changing this and that, trying it this way and that way, but nothing. When I finally got a signal, it was messy – lots of background “noise” – so I had to change the procedure bit by bit, and also change how I prepared my samples. Then the results were not showing any differences, so I then had to prepare samples from different time points. By changing things here and there, I got what I needed from the Western blots in the end. It was a rather tedious task, and took too long, but I made it through to the other side as it were!

Other experiments have been smoother, and others have been difficult like the Western. For example, initial polymerase chain reactions (PCRs) I did was generally fine, no huge problems, but when I started doing them again last autumn, I had contamination issues which proved to be tricky to solve. This was the case for real-time PCRs I did around that time too – took till Jan./Feb. till I got that sorted! So all in all this project was over two years of work, and I was so happy when I finished it all! – however, once you have a look at all the data and look at the story of the project, you’ll most likely have other experiments to do!

What I really want to say is, I think the hardest part of research is staying motivated; it's quite disheartening when you try everything you can think of, only to come out with nothing. It’s easy to lose motivation. So if you are currently in a similar situation, don’t be too disheartened – you’re not alone! I think that’s something important to keep in mind. It can feel like others are doing so much better than you, but please don’t compare yourself to others; probably the worst thing you can do if I'm honest! If you are concerned, talk to your supervisor - I'm sure it won’t be the first time they've encountered this.

How did I stay motivated? Well, I don’t think there is a “one-size-fits-all” approach here unfortunately! But I think the one thing that kept me going, particularly this time last year, is the fact that I wanted to find out the results. I wanted to know if what we thought was actually the case. However, this does not mean that I didn't have days when I was just distraught – I have cried a few times! I kept changing things in the experiments, and hoped that it worked. Essentially, I knew that I was not alone, and I knew that I had people I could talk to about this.

To people considering research/PhD; it is hard work, I won’t deny that. But at the same time it is rewarding, and I don’t regret going down this path at all, despite everything I've mentioned! It is also flexible, in that it doesn't matter when you work, which I like. And, you’ll be adding to existing knowledge, and possibly this could change things for the better – that is a big motivation for me, to think that one day the work I do may benefit people. Find what motivates you, and go for it!


 

Things to consider before applying for a PhD

📥  Faculty of Science, Maho, Postgraduate

I’m guessing a lot of you will be exploring options for your future, so I thought I’d make a list of things which I think are important when considering a PhD, and when preparing for a PhD interview.

Do you like lab/computer work?

As you might expect, we spend all our time working on our project, which means being in the lab or working at our computer all day. Now, you have to remember that this is not like doing practical classes, where the protocol is well established. There will be times when you spend months doing the same thing over and over again, with small modifications each day. Other times things will work perfectly the first time! Another thing to mention here is that the results are mostly unknown; I’d guess that majority of practical classes have been run before, so people know what to expect, but for me right now, I do experiments without knowing if the data will match the hypothesis. Therefore, it becomes quite tiring and difficult, and probably the best motivation is your love of lab/computer work! One good way of finding this out is, did you enjoy your final year project?

Do you like the sound of the project?

Ok, I’m not expecting you to know exactly what kind of project you would like! But look at the description; does that sound interesting to you? Do you think you will enjoy working on that project? Is the project in an area which you like? I would say choose based on the project rather than location, which may be difficult for some of you who have family commitments. Also, it doesn't have to be in a similar field to your final year project.

Find more than one potential PhD position.

PhDs are competitive – I have been turned down for two, and am not fully funded. As projects are often tied with funding, adverts will be going up regularly – keep checking! There will be more than one which will be of interest to you. Even if the application deadline has passed, that potential supervisor may get funding for another PhD student. Essentially, don’t give up if you are sure about doing a PhD!

Will your experience fit with the project?

For example, if you are not much of a computer person, will a bioinformatics project suit you? – if you are happy to learn how to code and work on a computer project, then great! But if you would rather be in a lab, then maybe that project is not for you. Also consider the kind of modules you have taken, or are taking; if you enjoy the biochemistry modules more, is an ecology project going to fit you?

Read at least one of your potential supervisor’s publications.

So, you have an interview – what’s the best way to prepare? I think the key is to get an idea of what that lab does, for example are they working on developing new ways of using genome sequences?  Pathogen evolution? Or are they working on animal development? A good way to get this information is to look at the papers your potential supervisor has published. And, you can impress them at the interview by letting them know you have read their recent work!

Meet the people working with your potential supervisor if you can.

The people who work with your potential supervisor, whether they be post-docs or PhD students, will be the people who you will spend most of your time with, so it is good to meet them if you can. This will also give you an opportunity to ask questions; how things work in the lab, what is it like working for your potential supervisor, what kind of experiments are commonly done, what is it like to live there (if you are new to the area)… perhaps take a look around the city/town. You have time, as you will be there for three-four years!