Author: Alethea Sara Mountford

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Archive Joe Crutwell

Antibiotics: Too Much of a Good Thing?

By Joe Crutwell

Do you remember a time before flatscreen TVs? How amazing they were when they first arrived?

Over time, we naturally adjust to advancements in technology. Imagine going back to a big, chunky TV now. Imagine having to wait until you got home or to a phone box to ring someone. Time has a habit of making us forget how difficult things used to be, and if we aren’t careful, some of those things could return very quickly.

Antibiotics, in one form or another, have existed since the early 20th century. The most well-known event involves Alexander Fleming’s apparent “accidental” discovery of penicillin. The story goes that he left a small dish of Staphylococcus bacteria (often a cause of food poisoning) near an open window, where it was by chance contaminated by a blue-green mould. When Fleming investigated further, he found that the mould was stopping the growth of the bacteria and breaking them down. The mould turned out to be Penicillium notatum, an experimental by-product which Fleming branded the now famous ‘Penicillin’.

 I have sometimes had to explain to flatmates that me leaving plates and bowls of unfinished food on the kitchen top to gather mould is not me being lazy, but actually an attempt to discover a new and potentially lifesaving treatment. You’d think I’d be outcompeted by modern pharmaceuticals companies and laboratories, who pour hundreds of millions of pounds into researching new antibiotic treatments. However there are not as many going down this research avenue as you’d expect. Why?

The simple reasoning behind this is that antibiotics are now something to be feared by many healthcare professionals and policy makers. A miracle cure-all that, with extended use, has revealed a darker and more dangerous side. Since antibiotics began being used large-scale (from approximately 1940’s onwards) a battle has been raging, unseen by most. A battle of resistance.

Penicillin and other later antibiotics were beginning to become non-functional. Higher volumes of these drugs were used, and the treatments began to be prescribed for conditions where they are not helpful, such as colds and other viral infections. This gave the bacteria a lot of exposure to the active ingredients of these medications, which is never a good idea.

Due to the rapid time to division and multiplication of bacteria (most infectious kinds average around 20 minutes), these organisms can evolve extremely quickly. Random changes in genetic information can by chance result in a single bacterium that happens to, for example, have a mutated cell wall that the drug cannot attach to or degrade.

If even just this one bacterium survives the antibiotic course, which it is obviously more likely to do, it multiplies and the infection begins again, this time with almost all of the bacteria having the ability to resist the drug. This process happening on the same bacteria treated with multiple drugs has resulted in ‘superbugs’ such as MRSA, a multi-drug resistant version of penicillin’s original enemy, Staphylococcus.

The World health organisation (WHO) launched World Antibiotic Awareness week this year (14th-20th November) to hopefully begin to educate people, both public and professional on the risks of antibiotic overuse. When turned to sparingly, and used appropriately, antibiotics can be an extremely effective tool against infections that would have previously been fatal. But without careful control, we may risk living in what WHO describes as “the post-antibiotic era”. Like TV, most of us have not experienced a world where antibiotics exist, and one glance at history tells us we probably don’t ever want to.

The WHO advise that ‘antibiotics are a precious resource’, and not a never-ending solution for infections, and it is up to everyone to ensure we do our bit in this new field of antibiotic conservation.

Links:
BBC history: Alexander Fleming
World antibiotics awareness week (WAAW)
WHO: Antibiotic resistance

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Archive Leonie Schittenhelm

Pooing Penguins and Bearded Biscuit-Dunkers

By Leonie Schittenhelm

Science is serious business. Why else would people toil over experiments until deep into the night, read papers until their eyes go red and devote their lives to researching the specifics a single protein?  And it can’t be denied that scientists have been given some really hard nuts to crack, from the specific health challenges of an ageing population to emerging viruses such as ebola. But sometimes it is nice to remember that science – in its very heart – is still about being curious about our everyday surroundings and trying to understand them to the best of our abilities. I here present to you five published papers that ask the real questions and finally give us the – sometimes surprising – answers.

  • An analysis of the forces required to drag sheep over various surfaces (Harvey et al., 2002)
    You might laugh now, but did you ever try to get a very unwilling sheep to get its yearly haircut? The trick seems to be a slightly sloped surface…

  • The nature of navel fluff (Steinhauser 2009)
    What the nature of navel fluff? This study brings us a bit closer to understanding this phenomenon and shows that old shirts produce more naval fluff than new ones. It actually hypothesises that naval fluff has a cleaning function? Pretty neat.

  • Pressures produced when penguins pooh – calculations on avian defecation (Meyer-Rochow et al., 2003)
    I’m sure these penguins from the coronation islands in the south Orkneys would love some information how to being covered in poo. Not sure how you might ever need this information, but make sure to check out the original paper – the figures are amazingly informative…

  • Microbiological Laboratory Hazard of bearded men (Barbeito et al., 1967)
    Apparently beards are able to harbour a variety of microorganisms you can pick up in microbiological lab – even washing merely reduces chances of unwittingly infecting others.

  • Physics take the biscuit (Fisher, 1999)
    Finally, the physical formula on achieving biscuit-in-tea-dunking perfection! Not always quite applicable maybe, the author advises that best results could be achieved when always having a thermometer on you for taking the exact temperature of the tea into account before dunking your digestive.

Reference List:

Harvey, J. T., Culvenor, J., Payne, W., Cowley, S., Lawrance, M., Stuart, D., & Williams, R. (2002). An analysis of the forces required to drag sheep over various surfaces. Applied ergonomics, 33(6), 523-531.

Steinhauser, G. (2009). The nature of navel fluff. Medical hypotheses, 72(6), 623-625.

Meyer-Rochow, V. B., & Gal, J. (2003). Pressures produced when penguins pooh—calculations on avian defaecation. Polar Biology, 27(1), 56-58.

Barbeito, M. S., Mathews, C. T., & Taylor, L. A. (1967). Microbiological laboratory hazard of bearded men. Applied microbiology, 15(4), 899-906.

Fisher, L. (1999). Physics takes the biscuit. Nature, 397(6719), 469-469.

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Amy Tooke Archive

North East Postgraduate Conference 2016

By Amy Tooke

On 24th and 25th November the North East Postgraduate Conference was held at the Great North Museum. It is organised by and for postgraduate students, and I was excited to go, especially as it was my first conference!

On Thursday morning I went to Professor Jenny Read’s talk “3D Vision in man, mantis and machine”, about her work in the Institute of Neuroscience at Newcastle University, on the mechanisms of 3D vision and its applications, such as in drone technology. I found Professor Read’s talk really interesting and entertaining. We got given 3D glasses so we could see the concepts being demonstrated to us and heard about how praying mantises have their own mini 3D glasses put on so that their perception of moving targets can be studied.

After coffee we headed over to the student presentations on Cell and Molecular Biology, where we heard about signal transduction in yeast, characterising Islets of Langerhans in the pancreas, gene editing, developing therapies for Duchenne Muscular Dystrophy in the heart, and using stem cells to treat a type of blindness. The talks were really engaging and it was great to hear about so many different areas of research.

On Friday I saw a talk from David Cork of Sirius Market Access “Why do science PhD graduates make good medical writers?”.  Sometimes when you’re in the university bubble you forget that there is a world of work for scientists outside of academia, so it was useful to think about what other skills can develop from a PhD.

Then I went to the student Microbiology presentations, which I’d been looking forward to as I’m a microbiologist. Students from several universities presented their work on a wide range of topics, from catalytic enzyme activities in the pathogen Staphyloccus Aureus to finding a target to use to diagnose pregnant mothers carrying Streptococcus so they don’t pass it onto their newborns.

Professor Stephen Hart from UCL GOS Institute of Child Health spoke about his research on using gene editing to develop treatments for cystic fibrosis; he explained how the team has been finding new ways to target the therapy to the lungs using nanoparticles. It was wonderful to hear about advances being made in this area of medicine and hopes for its future applications.

I went to the conference with some other MRes students, and we were really inspired hearing about the research going on around us from the student talks and looking at the posters. It’s really spurred us on to get back in the lab and start our own research projects!

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Archive Leonie Schittenhelm

How to grow a new retina

By Leonie Schittenhelm


Research at Newcastle University shows how algae-gels could lead the way in treating blindness with stem cell therapy

When Vanna Belton, a woman from Baltimore, was the first woman to regain her eyesight due to stem cell treatment earlier this year, excitement ensued. The possibility to repair diseased or damaged tissue using an individual’s own stem cells seemed close at hand. But while success of the treatment was undisputed, researching scientists can still not reliably explain exactly why improvement of eyesight in around 60% of patients occurs. Other studies have shown that reliably differentiating pluripotent stem cells into the coveted retinal cells, which are lost in many conditions leading to blindness, still poses a huge problem.

A group of researchers working alongside Prof. Majilinda Lako, Professor of Stem Cell Science at Newcastle University, have made a decisive step towards solving this problem. In a paper published earlier this month, they were able to show that growing human pluripotent stem cells in a gel obtained from brown seaweed significantly increased the amount of stem cells developing into pigmented retinal cells, similar to the ones found in the human eye. In addition to using the algae gel this was achieved by growing the cells in a so-called 3D culture, which had stem cells fully encapsulated within the gel for protection from external forces.

While stem cell treatment remains controversial, understanding how these cells could be safely and reliably used for therapy makes a tremendous difference and provides relief for people suffering from progressive sight loss. The Royal National Institute of Blind People (RNIB) predicts that rates of sight loss could increase dramatically within the ageing population of the UK, with estimates predicting the number of people affected by age-related blindness to double by 2050. Research in Newcastle will continue on this exciting topic, as it is hoped that the algae-gel could not only be useful for growing but also for transport and transplantation of retinal stem cells.

Check out the paper: Hunt, N. C., Hallam, D., Karimi, A., Mellough, C. B., Chen, J., Steel, D. H., & Lako, M. (2016). 3D culture of human pluripotent stem cells in RGD-alginate hydrogel improves retinal tissue development. Acta Biomaterialia.

 

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Amy Tooke Archive

The monk who grew pea plants: 150 years of Gregor Mendel’s laws

By Amy Tooke

2016 might be remembered for any number of reasons, but it also marks an anniversary of a major development in genetics. One hundred and fifty years ago, Gregor Mendel’s laws of inheritance were published. Mendel was an Austrian monk who painstakingly grew thousands of pea plants and counted the number of peas with certain characteristics. He came up with the concept of hereditary units that he named “factors” – or what we call genes today – and realised that there can be more than one version of each factor. Now, we call these versions of genes “alleles”. For example, a certain flower could have two alleles for colour, pink and blue.

By looking at the plants Mendel concluded that one copy of each factor is inherited from each parent. He outlined his ideas in his paper Versuche über Pflanzen-Hybriden (Experiments on Plant Hybridisation):

* The Law of Segregation
This law says that each parent contributes one allele when fertilisation takes place. Even though each parent will have two copies of a gene from their own parents, the alleles are “segregated” in the gametes (sex cells) so that there is only one copy per gamete. This means when the two gametes meet, there are two copies of each gene in the fertilised embryo.

* The Law of Dominance
If the two alleles are the same from each parent, the plant is “homozygous”, and will definitely show that trait, but if there are two different alleles (“heterozygous”), one version will be dominant and one will be recessive. The dominant allele will be the characteristic you see. So, if a plant inherits two pink colour alleles from its parents, it will have pink flowers. If the alleles it gets are one pink and one blue, and blue is dominant, it will have blue flowers.

* The Law of Independent Assortment
Leading on from the Law of Segregation, this law means that each pair of alleles is separated independently from the other pairs of alleles in the gametes – so you could have some alleles inherited from different grandparents in the gamete.

Mendel’s work didn’t have very much impact at the time; even Mendel didn’t realise its importance. The laws were rediscovered in 1900, and when combined with the idea that genetic information is stored in chromosomes in 1915, formed the basis of modern genetics. Where would we be today without the monk who grew some pea plants?

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Archive Jonny Bennett

Interview with Chi Onwurah, MP Newcastle Central

By Jonny Bennett

Photo: https://www.flickr.com/photos/MPD01605/6755068753

 

Chi Onwurah is not your typical member of parliament. Not only is she Newcastle’s first black MP, but she has had an impressive career in electrical engineering. Since training at Imperial College London, she has worked in industry for over two decades and travelled the globe. Elected as an MP in 2010, she was quickly identified as ministerial material, and now holds the office of Shadow Minister for Business and the Digital Economy. It goes without saying that very few of those sat in parliament can boast a background as diverse and as interesting as hers.

Her experience as an engineer not only makes her uniquely suitable for representing the North East, given its extensive industrial history, but has also given her insight into the way these industries do business within Europe. This has no doubt influenced her stance on the current EU debate, and we caught up with Chi so that she could explain why she has opted for the UK to remain in Europe.

Although staunchly pro-Europe, Chi says that, “I’m a proponent of a reformed, renegotiated relationship (with Europe)”. She cites that, Europe makes up our largest market for trade, but British MEPs often remain unknown and as a consequence, largely unaccountable. Chi attributes this to the fact that “a large segment of the population isn’t directly engaged with Europe”, and this may well be true; it seems likely that a majority of the population wouldn’t know who their MEP was, let alone their stance on European issues.

That said, it is her opinions on the common market that form the main basis for Chi’s argument. When we put it to her that other countries outside the EU, such as Norway, have access to the market, she rebuffs that, saying “they (member states) still have to follow and subscribe to standards without getting a voice”, alluding to the point that these countries don’t have representation in the European parliament. This view is certainly not without substance; it cost Norway an estimated £134 per person for access to the common market last year, yet they remain unable to influence the direction of policy within the market they compete.

It seems that her worries surrounding the common market are also shared by Chi’s ministry. “When we looked at a recent survey of digital start up companies, 82% were concerned that Brexit will damage their business… (there is) strong support in the tech, digital and science community that we’re stronger in Europe”.  Last month 50 local business leaders co-wrote a letter to the Newcastle Chronicle pledging their support for the UK to remain in Europe. This comes off the back of various other surveys, including one conducted for the leading scientific journal Nature, which found that of the 903 researchers surveyed, 83% would vote for the UK to remain.

Chi is also sceptical of Brexiteer’s claims that the UK would be a special case, observing that “campaigners of Brexit talk about full access to the market without free movement of people, yet nowhere else in the world is this the case”. This concern is justified; recent events in Switzerland saw them denied EU funding through the Horizon 2020 Initiative for refusing to ratify a freedom of movement treaty with Croatia.

With the EU referendum fast approaching, the eyes of European countries turn to the UK and concerns about the legacy of the referendum are being raised. Even if we vote to remain, what damage has been done in highlighting the depth and breadth of anti-EU sentiment? Chi too is worried, “it will make people question our commitment to Europe, and our place on the global stage”. Further repercussions could resonate in the years to come as European applicants choose to favour mainland European countries, which can offer a comparable standard of science, without the anti-EU feeling.

http://www.chroniclelive.co.uk/business/business-news/north-east-business-leaders-sign-11240750

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Archive Grace Laws

Modern-day Mummification: A Tool to Unravel Nature’s Physiology

By Grace Laws

Building upon the enormous success of the Bodyworlds exhibition, Dr Gunther von Hagens and Dr Angelina Whalley have brought to life the intricate features of animal physiology in their latest exhibition, Animal Inside Out. Aptly described as an “anatomical safari” with more than 100 plastinates on display, the exhibition enables an expedition of anatomy through the animal kingdom.

Plastinates in this exhibition have been created by the technique invented by Dr Gunther von Hagens. Plastination itself brings decomposition to a standstill, resulting in a completely sterile and durable specimen. The process begins by injecting formalin into the body, preserving it in the short-term and delaying the onset of rigor mortis. Dissections of the skin and connecting tissues allow for preparation of the anatomical structures. Next, liquids and soluble fats are immersed in a solvent bath. The solvent, e.g. acetone, replaces all of the liquids and fats that are otherwise problematic for preservation.  To replace the acetone in the body, a second exchange is carried out by vacuum impregnation with a reactive polymer. Following this, the body is positioned for display and hardened with gas, light or heat to finish the process. The total process is lengthy, with the average time for one plastination equal to a full year of work.

Addressing the rather large African elephant within the room, those interested in viewing the exhibition can rest assured that no animals were killed for the purpose of this exhibition. Animals have been donated through University veterinary programmes, zoos and animal groups. Although the prospect of plastination may be gut wrenching to some, the educational value of exhibits has enabled the acceptance of plastination in today’s society. The aim of Animal Inside Out is to encourage admiration and understanding of nature’s wonders. Fascinating evolutionary deviations of anatomy and organ function are highlighted, such as the powerful 11kg giraffe heart that is required to pump blood up its 1.8m long neck to the brain.  Organs from various species presented side by side allow an interactive comparison of physiology. The exhibition successfully and innovatively reveals the sophistication of anatomy to anyone interested.Animal Inside Out can be viewed in addition to on-going exhibitions at the renowned Centre for Life. A trip is definitely recommended. For more information on Animal Inside Out please visit: http://www.life.org.uk/whats-on/animal-inside-out For more information on Plastination please visit: http://isp.plastination.org/about.html

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Archive Becky Bramley

Inspiration from a Nobel Prize winner; Professor Sir Venki Ramakrishnan comes to Newcastle

By Becky Bramley

Scientist or non-scientist, everyone has heard of the Nobel Prize. It is often considered the “ultimate goal” of aspiring scientists, and remains one of the most prestigious forms of scientific achievement. Last Friday, Nobel Prize winner Professor Sir Venki Ramakrishnan popped into Newcastle University to give a talk which would mark the 5th Baddiley Lecture. This annual event celebrates the legacy of our very own Professor Sir James Baddiley who discovered a major class of bacterial cell wall components called teichoic acids. This has attracted several high calibre speakers in the past few years, including winners of the Nobel Prize, the Lasker Award and the Louis-Jeantet.

Professor Sir Venkatraman Ramakrishnan (let’s call him Venki) was introduced to the audience as a “quiet and modest man”. This is perhaps surprising given his list of credentials; the Nobel Prize for Chemistry in 2009, a knighthood in 2012, and President of the Royal Society by 2015. His contribution to the Nobel Prize was solving the precise structure of key components of the ribosome. This is a massive molecular machine (2.5 million Daltons worth) which translates our DNA into proteins, materialising our very being from our genetic information. As Venki elegantly describes, the ribosome “turns the blueprint of life into life itself”.

Nobody said it would be easy, and indeed the scope of the challenge is one of the things that drew Venki to this area in the first place. In his lecture, Venki described the toil of recruiting many post-docs to come “solve a subunit”, in a project with no guarantees of success. In an interview with The Guardian, Venki explains that “It takes courage to tackle very hard problems in science”. With pressure from competitors and funding stresses, it can be difficult to remain hopeful for the duration of such a difficult and ambitious project.

But this was no one-man job. In fact, solving the structure of the ribosome was a 40 year effort on the part of several research groups, and Venki shares his Nobel Prize with two other important scientists in the field. Indeed, Venki is quick to mention the key contributions of many other scientists who did not share in the glory of the Nobel Prize. The discovery is a good example of how collaboration can lead to great things in science.

Whether our ultimate goal is winning the Nobel Prize or simply obtaining a PhD, the pursuit of science takes risks – embracing uncertainty and persevering in the face of failure. Solving the structure of the ribosome helps us to better understand one of the central dogmas of biology, but this could not have been possible without endurance and the willingness to share expert skills and knowledge. So what does it take to really succeed in science? Collaboration over competition, and courage over convenience.

To read what Professor Sir Ramakrishnan has to say about his Nobel Prize: https://www.theguardian.com/science/2013/nov/24/venkatraman-ramakrishnan-ribosome-nobel-chemistry

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Archive Erin Cocks

From 3D light microscopy to 3D electron microscopy workshop

By Erin Cocks

I was recently given the opportunity to attend a workshop on 3D Light and Electron Microscopy and the Gatan 3View Users conference at the European Molecular Biology Laboratory in Heidelberg, Germany. Being my first experience at an academic conference I was excited to hear from those who have helped develop the electron microscopy discipline. From those who pioneered the first Serial-Block Face Scanning Electron Microscope, SBFSEM, to the new and upcoming developments or research being done across the globe. The technique itself allows for serial sectioning and imaging of a block of tissue, which can then be annotated or segmented and 3D reconstructions made of the tissue, like the example below.

An EM orthoslice of Guinea Pig Foetal Skeletal Muscle and the 3D reconstruction of the stack of images (Scale bar is 1µm), taken from my own research. The light blue is mitochondria, green the cell boundary, the pink is chromatin and the dark blue the nucleolus in the nucleus, which has been made transparent.

The topics discussed ranged from neural tissue to plant tissue 3D reconstruction as well as new ways to optimise the processing techniques for specific tissue types. One of the advances in neuronal tissue reconstructing is the ability to now do whole brain staining (Mikula and Denk, 2015). This means that large volumes of tissue can be reconstructed all from the same brain, leading to the reconstruction of an entire mouse brain. This is all part of the ongoing Connectomics project  http://www.openconnectomeproject.org/.  With these advancements in the technique we will only learn more and more about the brain and many other tissues.

A lot was learnt at the conferences, too much to put in a single blog post, and I am already looking forward to the next one in 2 years time and the other conferences and courses in between.

References

Mikula, S., and Denk, W. (2015). High-resolution whole-brain staining for electron microscopic circuit reconstruction. Nat. Methods 12, 541–546