Discovery at the Discovery Museum



Great Hall

Great Hall

Ready to replicate the success of last year’s Away Day, it was en masse outing time for ICaMB again! Time to find out who all the new faces are, and to find out exactly what that person you have a ‘hello and a nod in the corridor’ relationship with actually does at the bench all day. This year we headed to the Great Hall of the Discovery Museum. Despite the leaking roof caused by the downpour outside and the sometimes dodgy acoustics the day was still a success.

Serious faces, this is science

Serious faces, this is science

ICaMB is a fast paced, constantly evolving institute. Everybody is busy with their own research, making a break and a get-together once in a while a vital part of reminding ourselves of the vast range of expertise and diverse set of interests beavering away in our labs and offices. The answer to that tricky problem or that elusive technique is quite possibly just a few yards away.

But also fun!

But also fun!

With that in mind, this year’s Away Day felt particularly important as we welcomed 8 new academic groups to ICaMB from CAV (Campus for Aging and Vitality) as well new IRES fellows and a list of other recent recruits. Drs Victor Korolchuk and Gabi Saretzki from the CAV both spoke at the away day about their interests in neurodegenerative diseases and the role of oxidative stress in the ageing process.

As ever the day was kicked off by the Institute director, Bob (Professor Robert Lightowlers), who gave us a taster of ICaMB’s growth and success stories over the past year. Without breaking into the tune of that well known Christmas song; 7 Vacation Studentships, 6 BBSRC awards, 5 MRC awards, 2 Wolfson awards, 2 Senior Investigator awards and 1 Henry Dale ………. Not to mention all the promotions, outstanding research papers and commercial contracts = 1 happy Bob.











A cell-tastic morning then ensued: the completely dispensable nature of bacterial cell walls (Professor Jeff Errington); the role of NF-kB in the pathogenesis of lymphoma (Dr Jill Hunter); and the cell death independent functions of inhibitors of apoptosis (new IRES recruit Dr Niall Kenneth). The session was wrapped up by Dr Paula Salgado summarising 3.5 years of structural C. difficile research in 15min. Some feat Paula!

Of course just as last year, an absolute highlight of the day were the six, animated, three minute thesis presentations by our brave PhD students ……..  Soon to be followed by the look of horror on several Professorial faces when it was suggested by PAN!C that at next year’s Away Day we have a session of 3 minute PI pitches! We can’t ignore the demands of our PhD students now can we? And congratulations to Mandeep Atwal from the Cowell/Austin lab who against steep competition was awarded the prize for best three minute thesis.

The possibilities of alginate bread?

The possibilities of alginate bread?

A spot of oxidative stress and the evolution of peroxidases by Dr Alison Day, and some lunch completed the morning’s discovery. Though half an hour later and Dr Peter Chater had us all wishing we’d had an alginate packed lunch (and a go with the model gut!). Perhaps the Pearson lab can cater next year’s event? If it’s good enough for the One Show it’s good enough for the ICaMB Away Day.

A major focus of the Away Day is not just to learn about the breadth of exciting research carried out in our institute, but also to learn all about the very latest techniques and expertise ripe for exploitation. This year the focal point of new techniques came from Dr Alex Laude and the Bio-Imaging facility, with some beautiful images and super resolution microscopy techniques, which again left a number of the audience wanting a turn!

P1000375An afternoon transcribing and translating with Dr Danny Castro-Roa; learning about how the crucial nature of cell polarity means we really don’t mix up our arse from our elbow (thank you new IRES recruit Dr Josana Rodriguez); and last but by no means least, how on earth all that DNA manages to faithfully copy and repackage itself time after time from yet another new recruit, Professor Jonathan Higgins.

This completes our diverse and entertaining line-up, just leaving enough time for complementary wine, and the amusement as speakers and audience alike embarrass themselves at the ICaMB quiz (and I hear also in the pub afterwards).

One year of the ICaMBlog in numbers

By Neil Perkins

At the one year anniversary of the ICaMB Blog, and after publishing 35 articles, it seemed like a good time to reflect on what this initiative has (or has not) achieved. When Paula Salgado, Phil Aldridge and myself (with the prompting and encouragement of Bob Lightowlers) started this, there were a number of very clear goals we had in mind.  The first of these was to improve communication within ICaMB itself, so that we would all have a better sense of what our colleagues were up to, their achievements and to introduce new PIs.  In particular we wanted to highlight some of the great things our newly formed postdoc and PhD student associations (IPA and PANIC) have been doing. We also wanted to tell the world about some of the exciting science being performed in ICaMB and highlight some issues and discoveries that we thought would be of wide interest.  Finally we wanted to show the fun side of being a scientist in Newcastle and reveal some of what we get up to when we’re not in the lab.

Did we succeed?  Well that’s probably not for us to judge and the true test of this will be if the blog is still going in five years time (and if people are still reading it).  However, one unanticipated highlight for me has been the discovery of Google Analytics and what it can tell us about the success of the ICAMBlog. As a hard core geeky scientist, Google Analytics can be frighteningly addictive. A guilty pleasure for me has been to watch in real time what happens after we start publicising the latest blog: as soon as the emails get sent out, the tweets are sent or the Facebook update posted you can see people logging in to read the blog.  We don’t know who you are but we can see where you are and how you found us. Fascinating and slightly scary.

Each spike on the graph represents people viewing the website when a new blog article comes out. There is an immediate response the moment we send out an email, tweet or share on Facebook. Data shown is from Sept 1st - Dec 31st, 2013

So for this blog, to commemorate our one year anniversary, I thought I’d share some of the numbers. How many of you actually read the ICAMBlog?  Where are you from? Which article was the most popular?

So how popular are we?

At the time of writing we have had 7,703 ‘Unique Visitors’ to the blog, who have made 11,715 visits comprising a total of 20,602 ‘Page views’.  Unique visitors really means different devices, so someone who accesses the blog through their phone as well as a computer will count twice.  On the whole though, we are pretty happy with this.  It is thousands of people who now hopefully know more about ICaMB and what we do than a year ago.

So where is everyone coming from who reads the blog?  Unsurprisingly, the majority of our readers (58%) come from the UK.  The USA and Canada are the next highest, (although see the ‘reddit event’ below), followed by Australia and India.  Although the numbers are lower for other countries, the readership is truly global.

Within the UK, as might be expected, we have a large number of readers from the Northeast.  Readers from Newcastle upon Tyne represent 38.5% of our total readership which means that >60% of our readers are not local, so we are achieving our aim of getting the word out there.  London is the next highest city followed by several other cities with strong university links.

Someone from San Francisco just started reading the blog

What are people reading?

Our most popular article by far has been ‘Exploding Bacteria for Science’, which featured the work of Kenn Gerdes from the Centre for Bacterial Cell Biology here in ICAMB. This article garnered 3,189  page views, 15.5% of our total (note to blog team, must feature more exploding things next year). However, this number may be slightly artificial as it benefited from exposure on reddit (see what that means below). Our first ever long feature was ‘Bulging Bacteria and the Origins of Life’ which highlighted an outstanding Cell paper from the Errington lab on L-form bacteria. This is particularly impressive as the blog was starting and it wasn’t on people’s radar yet.  Completing our top 5 were the blog on ICaMB PhD student opportunities, the ‘Great Bacterial Bake Off‘ and ‘ICaMB goes away for the day’.

The success of Exploding Bacteria is also reflected in the number of views on our ICaMB Youtube site, with 3,186 visits to the penicillin effect video associated with this article.  Jeff Errington’s Bulging Bacteria video follows, with 322 views and the video of Jeremy Lakey and a new bacterial cell killer had a respectable 187 views, completing our top 3 video chart.

Are they really reading these articles?

One interesting feature of Google Analytics is that we can see how long people stay on each page, although we cannot control for people opening the page and then wandering off to do something else.

So when people from England and Wales log on, they spend an average of 1 minute 51 seconds with the page open.  They may be making tea of course but in general this suggests they are reading the blog.  Readers from Scotland and Northern Ireland, slightly less impressive, with 58 seconds and 1 minute 7 seconds respectively. Maybe they are speed-readers in Scotland.

When we look deeper, some of those page view numbers start to look a bit less impressive. All those visitors from the USA don’t look so good when you realise they stayed on the page for an average of 13 seconds.  Low attention span maybe?  It’s OK to say that, they will not have read this far down the page. Canada is a bit better at 34 seconds, Australia is at 24 seconds but India is a very respectable 1 minute 25 seconds. People from Newcastle spend 2 minutes 11 seconds on each page. London less so at 46 seconds while other cities average around 30 seconds.

Our headline numbers also start to look a bit less impressive when we take visit duration into account.  Of our 20,723 page views, 9,669 are for less than 10 seconds.  But that still leaves >8,000 page views being read properly. So a bit of a mixed bag but at least our colleagues seem to be interested in what we are writing.

The impact of social media

To get word of the blog to the outside world we have been using Twitter, Facebook and other forms of social media.  Google Analytics can also tell us how successful this has been. Of our 11,715 visits to the site, 1,284 have been through Twitter and 1,105 through Facebook. Twitter visitors stay for 1 minute 14 seconds on the site, while Facebook visitors stay for 49 seconds.

The reddit event

Reddit is a ‘a social news and entertainment website where registered users submit content in the form of links or text posts’.  Paula sometimes submits links to the science section when the ICAMBlog is carrying something that we think might be of interest.  This was certainly case with ‘Exploding Bacteria for Science’, which picked up a lot of traffic from reddit, accounting in part for its high popularity.  In total, we have had 1,557 visitors come through reddit and another 488 through Stumbleupon (‘a form of web search engine that finds and recommends web content to its users’).  These account for quite a large chunk of our USA traffic to the site. The down side is that the average visit duration of a Reddit user is 3 seconds, while someone from Stumbleupon lasts for 9 seconds.  I’m going to go out on a limb here and suggest that they are not actually reading the content.  So the moral is that while some approaches can boost our overall numbers, it is whether they stay around and actually read the articles that is important.

That big spike is people coming to the blog from reddit, staying 3 seconds and then leaving. The smaller spikes are our normal readership levels

Any Conclusions?

So have we been a success?  We think so but there is clearly a lot of room for improvement and scope to increase our readership. In the year ahead we certainly plan to continue our work on the blog and are very happy to welcome Suzanne Madgwick and Kevin Waldron to the blog team.  We will continue to highlight the science being produced in Newcastle but are thinking of broadening the scope of our articles.  For example, should we publish more opinion pieces and take a stand on the various issues confronting scientists today, both in and outside ICaMB?  We’d be very interested in hearing from you to let us know what you think. Comment is easy: tell us what you think and submit, no need to register or create an account. We would really like to hear from you, the reader that spends some time with us and reads all the way to end  – what kind of articles would you be interested in reading? Let us know!

A final word.  Those of us on the blog team would like to thank Phil Aldridge for all his help over the last year.  Phil has decided to step down from the blog after this first year but his input and enthusiasm has been crucial to getting things going and keeping the momentum up. Thanks Phil!

Leading the Way… in Protein Structure


By Kevin Waldron

This week, ICaMB welcomed the Leading the Way winners into our labs for an exciting day of science. As you may remember from our previous post a couple of weeks ago, Leading the Way was ICaMB and Leading Edge’s collaborative pilot scheme to take some of ICaMB’s great science (and early career scientists) into a local school, George Stephenson High School in Killingworth. That week was a great success, inspiring all of its participants: students, teachers and ICaMB members alike.

The overall winners during the week in GSHS were the AU team, made up of Lucy Hainsworth, Libby Macpherson, Rebecca Brown, Lauren Rhodes, Abbey Wrightson, Kimberley Stoker, Sophie Anson, Connor Little, Nathan Clapperton. AU designed an outstanding poster to illustrate how the prion protein represents a biomarker of mad cow disease (or, more scientifically, variant Creutzfeld-Jakob disease, vCJD), how the structure of this protein changes from the ‘normal’ form to the ‘abnormal’, disease-causing form, and how knowing the structure of the prion protein can enable us to design a diagnostic test.

AU’s prize was to spend a day in an ICaMB laboratory, learning about how we determine the structure of a protein, with the members of the judging panel, Dave Bolam, Paula Salgado and myself.

After a brief welcome and introduction, we kitted our guests out in fetching lab coats, supplied them with ‘Leading the Way’ lab books and got started.

Showing the kids how to plate cells on a petri dish


First, the kids tried their hands at microbiology with the Waldron lab, streaking E. coli cells onto agar plates and then picking colonies to inoculate cultures for recombinant protein production.



Practising to become a PhD student, staring at a pouring column…

Next, Dave Bolam and his team demonstrated how a His-tagged protein can be purified using affinity chromatography, and then the kids loaded each of their protein samples on SDS-PAGE gels. Remarkably, all of the students successfully purified their target protein, though it’s worth noting that this was not actually the prion protein, PrPC (Imagine the risk assessment!).


“Here, let me help you” says Dave.


It was great fun spending time with enthusiastic kids and giving them a flavour of what we do. It reminds you why you do science in the first place“, says Dave after taking part in this type of activity for the first time.

“We’re doing science now, Miss!” – shouted one of the students



The day finished with a demonstration of protein crystallisation with Paula Salgado and Will Stanley of the Structural Biology Laboratory. The students attempted to crystallise lysozyme (with mixed success), and then observed protein crystals under the microscope.

It’s always great to share our love for science with young minds and see them get really excited about carrying out the experiments we do routinely. It’s a breath of fresh air in the lab. Hopefully we’ve given them an experience to remember, as well as a better understanding of research in a biomedical institute.” commented Paula at the end of the day.


Although this was a high-paced tutorial in protein production and structure determination – a process that usually takes at least several weeks, and in some extreme cases an entire career – the students received a hands-on demonstration of some real-life research techniques. We all hope that this experience, even at such an early age, might just implant the idea of a future in science for some of these young people.

But from my own perspective, I can say that their enthusiasm has been infectious (no pun intended), and is a timely reminder of why I got into science in the first place – because at school I always found science classes more interesting than any others. I would have loved such an opportunity when I was that age.

Thanks go to Phil Aldridge, ICaMB’s Leading the Way coordinator, all of the members of the Waldron, Salgado and Bolam labs who helped out during the visit, the staff of George Stephenson High, and most of all to the members of the AU team, for making the day a success.


George Stephenson High School


An academic viewpoint on social media portals


We are, as a society, becoming inundated with comments that fall in to categories such as “did you see X on Facebook” or “Have you had a sneaky peek at that viral video?” and news articles such as this one. Here what I would like to do is pass on some of my own impressions and experiences of the benefits of using social media, focusing on Twitter and LinkedIN.


Yes, simply said, the impact science can make through such outlets presents a perfect opportunity with the drive to bring our research to the general public. Social media allows us all to interact with other scientists but, once you get going, the general public too, as we discussed here.


Technically, you do not need an account to read what’s going on; you also do not need a smartphone, any steam kettle of a PC or MAC will do.

I am in no way advocating that you join up. Have a quiet trawl through what science is on there, and maybe like me, you will make the leap! Discussing science in this format makes you think about what you say.

Being able to have a conduit that will generally be viewed by people interested in science but also has the opportunity to be picked up by a wider audience is what we are being asked to do in science. The amount of work needed to be a scientist on Twitter but not become an addict is, in my opinion, well worth it.

A good starting point is to read some of the blogs and transcripts from a fantastic episode that ran under #overlyhonestmethods during the first half of Jan 2013: has a number of active twitter accounts. Nature Reviews Microbiology (@NatRevMicro) regularly generates lists of papers of interest.

Microbiology Twitter Journal Club (#microtwjc). This is an organised twitter-based chat on microbiology every two weeks where a chosen paper is discussed. Recently, Microtwjc succeeded in gaining a response to one discussion by the authors of the paper – This is a form of public engagement exploiting social media portals and the group in question got free advertisement for their work!


I will openly admit I can not remember actually joining up to this portal. I, like many of us, continually get emails asking me to accept someone’s invite to their community. Recently, my ex-PhD student started looking for a more secure opportunity of employment. He and a number of others in the same position were given advice to maintain their LinkedIN profile. Exploit it as a professional digital CV, use its features to the maximum and, importantly, generate your own “linked in community” of people you know in science that can support your claims. This includes knowing how to pour gels, purify proteins and use seriously kick-ass microscopes or any other piece of kit we have access to! He got his current position due to his profile fitting a match during an employment consultation search.

This experience has given me a chance to see what its uses are. This means that my LinkedIN profile has gone from being an annoyance to something that is there to support my students and post-docs (if I ever have any again!) when they are actively looking for employment. Its not there for my own gain, its there so that they can state who trained/taught them and if someone wishes to, they can view my profile and look at my own career history.

My social media timeline:

I have been on Facebook since 2009. I joined Twitter in March 2012 and this will be my second date with blogging.

I joined Facebook for a very specific reason. I had the amazing opportunity through a joint Royal Society and Daiwa foundation International Project Grant to visit my Japanese collaborators for 3 months. It was agreed that we would keep our family up to date with our antics by exploiting Facebook’s method of publishing photos.

I joined Twitter through a friend posting tweets to Facebook: these included what was floating their boat on new papers, commenting on science articles in the press and generally having science-based discussions with other scientists. I made a decision from day one Twitter would be for science (hahaha!). What do I have now? Well, I do focus on Science and I follow a good group of science communicators across the UK and US. I also seem to be following many of the real ale bars of Newcastle upon Tyne!

Image Sources: Here and Here