Meet the Scientists

On Saturday 17th March IIB led the Meet the Scientists Event at the World Museum. Activities included stands led by the CCI and Madine group from IIB along with other stands from Life Sciences, ITM and IGH.

The CCI had a large team, and all worked together brilliantly on the Seeing is Believing stand! The team included:

Violaine See (CCI staff): Preparation of samples for imaging, and assistance at the event.

Dave Mason (CCI staff): Preparation of samples, imaging of samples, produced posters for the event, and assistance at the event.

Marco Marcello (CCI staff): Organisation of virtual reality tours of microscopy images, with Virtual Arcade

Daimark Bennett (CCI staff): Preparation of samples for imaging, and assistance at the event.

Raphael Levy (CCI staff): Preparation of samples for imaging, and assistance at the event.

Anne Herrmann (Postdoctoral researcher): Imaging of samples, preparation of printed materials for the drawing microscopy station.

Sophie Cowman (PhD student): Filmed and produced a tour of the CCI facility, which was on display during the event.

Rebecca Kelly (PhD student): Preparation of CCI postcards, set up and take down of stand, and assistance at event especially for the match the picture quiz.

Claire Kelly (PhD student): Set up and take down of stand, and assistance at event especially for the virtual reality microscopy tour.

Hammed Badmos (PhD student): Preparation of samples, and assistance at event especially for the microscope demonstrations.

Jen Francis (PhD student): Assistance at event especially for the microscope demonstrations.

Sumaira Ashraf (Postdoctoral researcher): Set up and take down of stand, and assistance at event especially for the microscope demonstrations.

Jen Adcott (CCI Staff): Organisation of the Seeing is Believing stand and co-ordinator of activities, imaging of samples, designed and produced the match the picture quiz and microscopy stickers, and assistance at the event.

Feedback from the CCI stand, seeing is believing:

Violaine See – “It was great, and the activities were all very popular. What I really liked about our exhibit is that it was real science. Well done Jen A for leading this, the result was absolutely awesome. Well done Jen F, Hammed, and Sumaira for guiding the kids with the microscopes with so much patience and enthusiasm. Dave has been an absolute star with the colouring sheets and at explaining what we do with microscopes. Rebecca and Claire have been fantastic with the quiz and virtual reality. An amazing team effort. I feel very fortunate to have you all around, you are amazing.”

Daimark Bennett – “Fantastic effort by everyone and great activities – it was great to see how busy it was even later on. The VR clearly went down a storm and everything from the stickers to the CCI movie looked really professional and well put together. It really is hard to convey the science when it’s so chaotic but I think the exhibit was pitched at the right level. In any case, my daughter, who is not easy to impress, gave the thumbs up 🙂 Well done everyone!”

Jen Adcott – “It’s great to work with such a fantastic team of people! The day was busy, and the CCI stand seeing is believing was hugely popular with many repeat visitors. I am looking forward to meeting more future scientists at the next events.”

The Madine group ran 2 activities ‘How does the heart work?’ and return of the popular ‘A lego treasure hunt for new medicines!’ with the help of PhD students James Torpey and Nathan Cumberbatch, MRes student Kiani Jeacock and undergraduate volunteers.  Visitors enjoyed learning how blood is transported around the body by watching blood cells flow around the giant circulatory system (borrowed from IACD created with a Wellcome Trust Public Engagement award, granted to Dr Valentina Barrera). Children of all ages were keen to take part in the Lego treasure hunt around the museum to find the correct drug that fit the Lego protein molecule, and be rewarded with a Lego Scientist to take home. Thanks to members of the group for their help and enthusiasm when describing the drug development process through the use of Lego.

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Shrewsbury School visit

The Lower Sixth Biology visited the Institute for Integrative Biology.

With a world-class biological research facility only a couple of hours away, it would seem silly for us not to pay them a visit each year, and once again we were generously hosted by Professor Alan McCarthy – Head of Undergraduate Admissions for Liverpool’s School of Life Sciences (and Shrewsbury School Governor). In the morning we heard talks giving overviews of the key technologies we would later be seeing.

You can read the rest of their visit report here.

 

 

 

Quantum dots for Immunofluorescence

Guest post by Dave Mason; reblogged from rapha-z-lab

In modern cell biology and light microscopy, immunofluorescence is a workhorse experiment. The same way antibodies can recognise foreign pathogens in an animal, so the specificity of antibodies can be used to label specific targets within the cell. When antibodies are bound to a fluorophore of your choice, and in combination with light microscopy, this makes for a versatile platform for research and diagnostics.

Most small-dye based fluorophores that are used in combination with antibodies suffer from a limitation; hit them with enough light and you irreversibly damage the fluorochrome, rendering the dye ‘invisible’ or photobleached. This property is the basis of several biophysical techniques such as Fluorescence Recovery After Photobleaching (FRAP) but for routine imaging it is largely an unwanted property.

Over 20 years ago, a new class of fluorescent conjugate was introduced in the form of Quantum Dots (QDots); semiconductor nanocrystals that promised increased brightness, a broad excitation and narrow emission band (good when using multi-channel imaging) and most importantly: no photobleaching. They were hailed as a game changer: “When the methods are worked out, they’ll be used instantly” (ref). With the expectation that they would “…soon be a standard biological tool” (ref).

So what happened? Check the published literature or walk into any imaging lab today and you’ll find antibodies conjugated to all manner of small dyes from FITC and rhodamine to Cyanine and Alexa dyes. Rarely will you find QDot-conjugated antibodies used despite them being commercially available. Why would people shun a technology that seemingly provides so many advantages?

Based on some strange observations, when trying to use QDot-conjugated antibodies, Jen Francis, investigated this phenomenon more closely, systematically labelling different cellular targets with Quantum dots and traditional small molecule dyes.

Francis_et_alFig3_GM

Figure 3 from doi:10.3762/bjnano.8.125 shows Tubulin simultaneously labelled with small fluorescent dye (A) and QDots (B). Overlay shows Qdot in green and A488 in Magenta. See paper for more details. 

The work published in the Beilstein Journal of Nanotechnology (doi: 10.3762/bjnano.8.125) demonstrates a surprising finding. Some targets in the cell such as tubulin (the ‘gold standard’ for QDot labelling) label just as well with the QDot as with the dye (see above). Others however, including nuclear and some focal adhesion targets would only label with the organic dye.

2190-4286-8-125-graphical-abstract.png

The important question of course is: why the difference in labelling when using Quantum Dots or dyes? This is discussed in more detail in the paper but one explanation the evidence supports is that it is the size of the QDots that hinder their ability to access targets in the nucleus or large protein complexes. This explanation further highlights how little we really know about the 3D structure of protein complexes in the cell and the effect of fixation and permeabilisation upon them. Why for example, can tubulin be labelled with QDots but F-actin cannot, despite them both being abundant filamentous cytosolic structures? At this point we can’t say.

So why is this study important? Publication bias (the preferential publication of ‘positive’ results) has largely hidden the complications of using QDots for immunofluorescence. We and others have spent time and money, trying to optimise and troubleshoot experiments that upon closer study, have no chance of working. We therefore hope that by undertaking and publishing this study, other researchers can be better informed and understand when (or whether) it might be appropriate to use Quantum Dots before embarking on a project.

This paper was published in the Beilstein Journal of Nanotechnology, an Open Access, peer-reviewed journal funded entirely by the Beilstein-Institut.

 

Marvellous Medicine at Meet the Scientists

Guest post by Rorie Hather

Meet the Scientists” is a regular programme of events that takes place at the World Museum Liverpool and organised by the University of Liverpool’s Faculty of Health and Life Science with the support of the Wellcome Trust.  On Saturday 26th November the event drew again a large turnout of visitors. The overall theme was “Marvellous Medicines”. It focused on where our medicines come from, the different methods we use to treat diseases as well as the future of modern medicine. The day involved research teams from across the University of Liverpool lending their time and resources to run eight interactive stalls aimed at ensuring a fun and informative day for the whole family, regardless of age.

Two stalls out of the eight stemmed from different research teams within the Institute of Integrative Biology.  Dr. Raphaël Lévy’s team together with colleagues from the Institute of Translational Medicine (Toni Plagge and his student Joe Robertson) had a stall on “stem cells and nanoparticles”. Dr. Madine’s amyloid group utilised Lego pieces to show how proteins interact with one another and how this impacts their research into neurodegenerative and cardiovascular amyloid diseases.

gold

Golden? The beautiful colours of gold nanospheres and nanorods in water. The infrared absorption of some of these nanomaterials can be used to image cells in tissues.

The stem cells and nanoparticles stall attempted to translate the ongoing UK Regenerative Medicine Platform work into interactive games to help understand just how small nanoparticles are, as well as showing where stem cells are found within our body and the possible contributions they may be able to have to modern medical science.

A “pin the organ on the human” game was also run, involving visitors placing organ cutouts onto an outline of a human they drew onto a whiteboard, hopefully in the correct place. This game helped to show where exactly our organs are located, and how they each hold stem cells vital to our ongoing health and regeneration. (The freely available resources developed by Eurostemcells are available here if you wish to try this yourself.)  In total, 7 people help run the activity throughout the day: Sumaira Ashraf, Joe Robertson, Elizabeth Grimes, Joan Comenge, Rorie Hather, Angela Midgley and Raphaël Lévy

Dr. Madine’s group used a highly popular tactic among many of the younger visitors. Their game, invented by Kieran Hand and James Torpey, involved using Lego pieces to demonstrate how small molecules can dock to target proteins implicated in the diseases they research. Children were sent on a scavenger hunt around the different stalls to find the hidden complementary shape of Lego that would fit to their existing protein. On their stall, PhD student Kieran Hand said one of their aims was to raise awareness of light chain amyloidosis – a disease that is often left out of the limelight, yet impacts a similar number of people as motor neurone disease. The prizes that had been assembled to give to children who were successful in the drug discovery hunt ran out by 2 pm, showing just how busy the event was. Hammed Badmos also helped on the stall during the day.

The Meet the Scientists series continues into the new year, with the next event, “Brainiacs”, taking place on the 21st January 2017. It will explore the complexities, faults and cures that surround the human brain.

Find out more about future events here.

Institute of Integrative Biology away day

Thursday the 24th of November, the Institute of Integrative Biology had its away day at the Crypt of the Metropolitan cathedral. The event was packed with good science from molecules to ecosystems. Some of the highlights of the day were captured via Twitter by the attendees using the hashtag #iibawayday. Below is a summary of the day via these Tweets (Storify).

11 Nuffield students visited IIB this summer

This past summer, the Institute of Integrative Biology has once welcomed Nuffield students, just, many more than last year. Thank you to Jane Hurst, Michael Gerth, Philipp Antczak, Violaine See, Luning Liu, Dave Mason and Raphael Levy for providing these placements.

 

 

Shrewsbury School visit for Life Sciences Technology Day @tsm_biology

Guest post by Dr Torin Morgan, Head of Faculty, Shrewsbury School

Shrewsbury School

RAJC and his set listening to PhD students explaining the use of mass spectrometry to identify proteins at the University of Liverpool’s Centre for Proteome Research

On Friday 6th November all Lower Sixth Biologists took a day out to visit the University of Liverpool’s Institute of Integrative Biology. We were hosted by Professor Alan McCarthy, one of the UK’s leading microbiologists and the Head of Admissions and Recruitment for the School of Life Sciences (and also a Governor of Shrewsbury School).

Biosciences in the 21st Century are increasingly focused on understanding the information contained inside living cells in the form of DNA (the ‘genome’) and proteins (the ‘proteome’).  Pre-U Biology places great emphasis on practical applications and so this visit was a tremendously valuable opportunity to for us to see the cutting-edge technology being deployed by this world-leading research department.

In the words of some of our pupils:

“The trip to Liverpool University was an interesting and memorable experience. We had a full morning of lectures before attending tours. The lectures were pretty fascinating, even though the topics the speakers touched on were slightly above our understanding. The final lecture by Prof Rob Beynon (Head of Biochemistry at the University) really caught my attention, as I never knew proteins play such a major role in sustaining our lives. After a brief break, we were taken on tours. We saw some high-end technologies being used by both researchers and students. Quite a few of us were astonished by how expensive the equipment was (£800,000 for a next-generation DNA sequencer!). In the final tour, we met Mike – a student who was about to get his PhD in biology. Apart from explaining how he managed to crystallise proteins to study their structure, he told us what being a student at a university is like and gave us some useful advice on how to make the most out of it.”

“The lectures were on a variety of topics. Most were about the advanced techniques used to understand the processes going on inside cells; there was also one by Dr Raphael Levy on the way evidence is misused by the media (especially the Daily Mail!) to report and distort news of scientific discoveries. He reminded us to always ask for evidence! (http://askforevidence.org/index)”

“I found the tour of the x-ray crystallography laboratory especially interesting. Researchers can now generate a three dimensional image of a molecule by using x-ray crystallography. The molecule causes x-ray beams to diffract in different directions and this data can then be used to construct and image of the molecule.”

“One aspect of the day that I found particularly interesting was cell imaging. Following a colourful and inspiring lecture delivered by Dr David Mason, we acquired a new understanding of how we can view cells and observe their features. The lecture certainly lived up to its name, ‘Seeing the world in 5-dimensions’: after covering the obvious first 3 dimensions, XYZ, a splash of colour and the element of time brought the images to life.”

“The most incredible technique I saw was laser capture microdissection, in which an individual cell was shown being cut from a sample using a laser before being propelled (again by the laser) into a waiting test tube. This tiny, targeted tissue fragment could then be subjected to DNA sequencing!”

Whatever their level of interest in Biology, the pupils will find themselves thinking back to the trip over the coming days and months, and, as it keeps resonating with theory in their Pre-U course, their appreciation for what they saw will grow.