Most summers we have around 20 students working in the Microbiology and Molecular Biology lab, SB209, in the Science Building on the Brayford Pool campus. This is a place for those students to share their experience.
Author: Nicola
//First day in the lab, and it’s great to have it full of people so keen to get on with some research! I hope you’ve all had a good day, although I suspect you felt it was very unproductive! Paperwork tomorrow, and then on Wednesday we’ll actually be able to get on and do some sampling!
//So if you’ve not done any kind of research project before, I suspect you’re going to be completely blown away by how long everything takes and how much you have to do before you can actually get anywhere with getting your hands dirty. When you walk into a lab for a practical, equipment and consumables have been ordered, paperwork has been photocopied, solutions and stocks have been prepared for you to work with, and the administration for ensuring your health and safety has all been done for you. When you’re doing your own data collection, all of those parts, normally carried out by your administrators, finance managers, technicians and academics, all becomes your responsibility. This is known as ‘research governance’.
On the first day, I will be teaching you how to make up stock solutions and agars and how to keep the lab clean and tidy – the technicians will not sweep in and dispose of your dirty tips and wash out your glass bottles this summer. You may be surprised by how much effort it takes to keep on top of this.
Also during that first day, while the solutions are autoclaving (it takes three hours, so we have some time to kill), I’ll be talking to you all individually, or in small groups, helping you plan the project you are going to carry out and what you will need to put in place to ensure it happens safely and ethically. This means carrying out ethics approval and risk assessment to ensure you will be safe while working, and planning your methodology to make sure we have all the equipment and consumables you need already available to us, (otherwise we will have to do some ordering).
By the end of the first day, you should have a clear plan in your lab books for the summer (don’t forget to bring a hard backed note book specifically for this work!). That means on the Tuesday, (when I can’t be in the lab, which means you can’t because you haven’t carried out the risk assessment!), you can spend the day filling out the paperwork to make sure that from Wednesday we are properly covered in the context of research governance.
This is the experience that I want you to get this summer. Being blunt, the data collection bit is the easy part, and won’t really teach you much at all – the techniques you will be using have all been taught to you in the past through practicals. I will have succeeded in making your summer experience a useful one if you walk away thinking ‘wow, if only I knew then what I know now’. It is these experiences that will make you a good scientist, and will put you in the best position for your future studies.
//Another Monday morning, and my inbox is full of emails to tackle ahead of the new week! One of those emails is from Student Opportunities which explains how I get you enrolled on the campus jobs system so that you can work outreach events over the summer. I will soon be emailing your names over to them so they can send you the paperwork you need to complete in order to apply for jobs. Don’t forget that once you are on the system you can also work open days in the new academic year, so make sure you get the forms processed asap!
//Outreach is a really important part of my life, and of course it is also part of my job! I have been doing outreach in one form or another since I started at the University in 2003, and my involvement has only grown since then. I started with a few school visits as part of a recruitment drive for the Forensic Science degree, and it has now grown into multiple annual local school events and talks and activities around the county and even the country for the Women’s Institute (WI), University of the Third Age (U3A) and Graduate Women’s groups.
Outreach is so important as it plays a fundamental role in demystifying science for the general public. We hear too much these days about a lack of belief in ‘experts’ and a lot of that has to do with scientists standing up and saying incomprehensible information in technical jargon that is supposed to scare or intimidate people. For me, there is nothing better than the ‘lightbulb moment’, which is what drives me every day as an educator, and good outreach can ensure that we can get our message out simply and effectively, and from there it can spread further.
This summer, as always, I have signed up for and booked in a large number of outreach events, and while I will be involved in them all, I also need support to ensure they run smoothly. For them to work effectively I need passionate, dedicated and hardworking helpers who believe, as I do, that outreach is one of the most important things that scientists can do. If that is you, then I will look forward to working with you. The process for signing up is relatively long-winded, and will involve having right to work checks, completion of information regarding payment, applications for roles and possibly job interviews, but I will try and ensure that any of those who are keen and fit the profile will get a chance to have at least some of the opportunities.
When I know the process I shall add the information here, so keep a lookout, and of course, make sure you blog about your experiences doing the outreach!
Nicola
//Summer 2017 is upon us, and I’m about to add the next batch of summer students to the pages so they can share their experiences
//https://m.youtube.com/watch?v=am3iGHDnJHc
Welcome to the lab. Here’s an awesome video to start us off!
//Thought I’d have a quick update to see if I can manage to write a normal post now!
//It’s been a while since this has been updated as last year we couldn’t have our standard summer experience because the science building was being renovated. But we’re back on track this year, and should have lots of exciting research to share. Some of those joining us will also be carrying on throughout the next academic year on their final year projects, so I’m hoping they’ll keep us updated here as well. Remember that this is an informal process and should be used to share all of your experiences, good and bad, and do comment on others posts if you have any ideas and suggestions.
//Exam boards are nearly over, so I’m really hoping I can get back into the lab soon. I’m about to put a request into my son’s school newsletter for donations of old shoes with Velcro straps for my latest research idea (looking forward to seeing preliminary data!), and with Laura churning out data on fibres in cat coats, and another research plan developing to resuscitate a three year old final year project, I maybe on line for three papers this summer!
//So good to hear so much form you, Faris, please keep going! I would love to hear from the rest of you as well though, so I can keep updated on the research going on. I’m hoping I’ll be able to start updating regularly soon as well, as I get boards out of the way!
//Just a quick update to say hello again, and hope that you manage to get online and blogging now! Following the session this afternoon on forms, have a go at filling them in as best as you can, and then bring them into the lab to show us what you’ve managed. Use this summer as a way of finding out as much as you can about the behind the scenes parts of scientific research, as this is the area that will put you way ahead of the game in September!
As for my research, I’ve only just managed to sub on my E. coli strains today that I grew on Thursday of last week, so it’s been a slow start!
//Welcome to all our new students, and welcome back to those who contributed last year. Do please introduce yourself and let us know what you’re working on here, and keep us updated with your progress.
This year I’ll carry on with some of my plasmid stability work, but I’m also working on background fibre research, with the hope of getting a couple of papers out – watch this space!
//Taking this opportunity to share Mike’s blog at http://themolecularlab.tumblr.com/ which covers a lot of really relevant info on molecular biology, including PCR with details on primer design, and other areas. Critical reading for any students who are working on molecular biology projects.
//Wonderful new website from Randall Monroe – creator of xkcd – proving that physics can be fun! www.what-if.xkcd.com
//On a slightly different note, if you want to be correct, and use italics (or bold, or underline) in posts for names, you’ll need to learn a little bit of html coding:
for italics, you need to use the i tag, in triangular brackets – just like this:
<i>E. coli</i>
Bold = b
Underline = u
Subscript = sub
Superscript = sup
Bullet point list = ul and li (a little trickier – check for a tutorial online)
Hope this is useful!
//Most of you have probably heard me going on about my PhD research. A quick overview here though, just so you’re all up to speed. Antibiotic resistance is an increasing problem – I’m sure you’re all aware. New antibiotics are rare discoveries these days, so we need new options. Plasmids are small extrachromosomal pieces of DNA, and often carry antibiotic resistance. They are also often very stably maintained with the bacterial cell, ensuring that this resistance is passed on through generations. The logic goes that if we can prevent the plasmids being inherited, we can remove the antibiotic resistance, and be able to treat the infection again.
For my PhD thesis, I was provided with four plasmids with different stability levels, all of which encoded resistance to ampicillin. My work was to study the effect of this reduction in stability as a model system, and see whether destabilised plasmids would reduce the effectiveness of a cell culture to survive in the presence of ampicillin. I also modified and cloned a series of plasmids with the same stability levels, but with resistance to chloramphenicol.
Generally, it went well, although there were more questions raised than answers provided, which is why it is critical that this work starts again, so we can get the data we need to move forward. Unfortunately it has been over 10 years since I was working regularly on the plasmids, and some have been lost, and others have been contaminated and damaged.
Sophie and I will be working hard over the next few weeks to revive as many of the original plasmids as we can, and recreate the ones that have been lost. It’s off to a good start though – this is a plate of E. coli DH5a cells containing the pOG4 plasmid, proved by the fact that the cells are surviving on a plate containing ampicillin. 1 down… 7 to go…!
//
One of the most important jobs in a microbiology lab is maintaining a culture collection to ensure all the bacterial and fungal strains necessary for research are kept pure and thriving. Unfortunately, without a consistent research programme, this often doesn’t happen in our labs. I need a couple of very specific E. coli strains for my research, but I came back in at the start of this research period to plates for these strains like the first one in this picture of DH5a – almost a year old, so completely dry and, to the unobservant, useless. But, with a little encouragement, I got the few cells out alive as you can see in the second plate, and then within another day to the pure streak in the last plate.
Unfortunately, I wasn’t so lucky with my second strain, C2110, and I’ve had to revert back to a stab culture I finally unearthed, but hopefully I should see growth this morning when I get into the lab.
As a result, I’ve got some of you working on creating a culture collection of some of the random bottles of cells I’ve found lurking around in the incubator room, by creating slopes and stabs for storage. It will really be a revelation if we can get it all sorted out!!
//Just something to think about – being able to innovate and create novel data as a scientist is about being able to adapt, alter and invent methods to gain new results. Therefore, if you don’t understand the methods you’re using, you can never advance. You’ve probably never really done it before, as I suspect you’ve just blindly followed the provided SOPs, but from this point on, start digging deeper into the science behind the experiment. Learn about the function of every chemical, of every physical action, and you’ll be able to understand why the experiment works the way it does. That is all I do, and that is the main reason why I can make suggestions of change when things aren’t working.
//Starting to get set up in the lab now – another week and we might get some interesting results to post!
1. Alkaline lysis solutions made up, ready for plasmid extraction for the stability plasmid experiments for Sophie. Struggling with getting my E. coli cultures revived after they were left to die off in the fridge, but I’m confident I’ll get them back.
2. Lysis buffers set up ready for bulk NA extraction from dog testes (tomorrow’s activity) so everyone can have a go at some guaranteed successful gel electrophoresis results before getting stuck into the much more temperamental PCR experiments.
3. Plates from water from the Brayford Pool incubating – planning on getting some prelim data on total viable counts from the pool on a more or less daily basis for Ryan, to help him plan sample sizes when he gets started. Also got the MLSA plates made to start culturing E. coli for Rosie.
4. Box of random fibre samples located and tidied a little, so back on with the plan of writing a book of images for forensic fibre analysis, and revisiting some of my final year students projects to see if I can get publishable data with a few more experimental repeats.
That’s my round-up – what about yours?
//You all know me – I’m Nicola (Nicki or Nic, or in extreme circumstances, Dr. Crewe), and I teach on the Forensic Science, Biomedical Science, Human Nutrition and Biology courses at the University.
This summer I made the (slightly crazy) decision to allow any students who had the guts to ask to come and join me in the lab for the summer to carry out research. There are a wide variety of projects taking place, and a substantial amount of funding has been secured to carry out the work.
This blog is a side project of mine, to document the highs and lows of the summer lab experience for all involved. I believe this will be inspirational, and certainly very interesting and educational.