This week, Catherine Yu shares her  experiences of working at the University of Sheffield MBB department and the Florey Institute over the summer as part of Princeton University's the International Internship Program. 

​The Florey Institute at the University of Sheffield has been hosting students from the International Internship Program over the summer months. This program is an opportunity for students from Princeton University to take part in internships across the world. Our students have been working hard and Julia Edgar has taken some time to tell us about her experiences of the UK.
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Last month, Florey Institute members Dr Claire Turner and Dr Thushan de Silva travelled to the MRC Unit The Gambia at LSHTM for the first collaborators meeting and symposium for group A Streptococcus in West Africa. 

​They were joined by Dr Annette Erhart, Prof Martin Antonio, Dr Abdul Karim Sesay, Prof. Beate Kampmann, Dr. Anna Roca and Dr Edwin Armitage from the MRC Unit The Gambia at LSHTM, Prof Pierre Smeesters from Universite libre de Bruxelles, Belgium, Dr. Soumeya Ouangraoua from Centre Muraz, Bobo Dioulasso, Burkina Faso and Dr. Abdallah Sonko from Hôpital pour enfants Albert Royer, Dakar, Senegal. This was the first face-to-face meeting of all those involved in the GCRF ODA, University of Sheffield funded project on group A Streptococcal Pyoderma in The Gambia ‘SpyDERM’ and the MRC BactiVac Network funded project Molecular Epidemiology of Group A Streptococcus in West Africa (MEGAS).

​RHD is a significant cause of cardiac morbidity and mortality in The Gambia with group A Streptococcus (GAS) being the trigger for this post-infection immune sequelae. Skin infections (pyoderma) may be more commonly associated with RHD in this region compared to pharyngitis in other countries. There is remarkably little data on the molecular epidemiology of GAS isolates from West Africa, which makes assessing regional suitability of vaccines in development extremely difficult. Through the collaborations that have now been formed between the Florey Institute in Sheffield, Belgium, The Gambia, Burkina Faso and Senegal, we will be providing crucial epidemiology and molecular insight into GAS disease in West Africa, supporting the development of a desperately needed vaccine.

​​The meeting provided project updates and inspiring research presentations and discussions. The week ended with a workshop on Bioinformatics hosted by Dr Claire Turner and Saikou Bah. Saikou is a Gambian post-doctoral scientist and bioinformatician, who will be joining the University of Sheffield in July as a GCRF post-doctoral fellow working with Claire and Thushan to explore the pathogenesis of GAS isolates from The Gambia and UK. 

The Florey Institute is delighted to have been featured at the Medical Research Council (MRC) Festival of Medical Research in Sheffield. The event took place on 15th and 16th of June, in the Winter Gardens and Norfolk Heritage Park respectively. The theme of the festival was ‘Fighting the good fight: how medical research helps us combat disease', and it aimed to showcase the diversity and latest medical research at the University of Sheffield.
 
A team of students from the Florey Institute, led by Yin Xin Ho, Dan Bennison and Dr. Daria Shamarina introduced you to the concept of the microbiome and immune system through various activities. We demonstrated this with a display of face microbiome from different volunteers. To explain the immune system and how it helps us fight infections, we prepared microscopic slides with white blood cells such as neutrophils containing S. aureus. We also discussed about the research in the Florey Institute, and how researchers with different backgrounds such as biology and physics work together to understand and fight against infections.
 
To know more about our research, please feel free to visit our website and to follow us on Twitter.  If you took part in our microbiome plate activity then you can find all the pictures by following the link below, just look for the number we gave you on your ticket!  

https://drive.google.com/drive/folders/1e97JWKQwXoU_bJoO3AcZ2UrKaBSQZaz8
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​Last weekend, the Florey Institute visited the Inverness Science Festival and we hope you had as much fun as we did. In conjunction with The Microbiology Society, our volunteers took along a number of engaging and illuminating activities, geared around getting you up close and personal with your very own microbiome.

The team, led by Dr. Daria Shamarina, introduced you to the concept of your skin as a living, breathing protective barrier. We showed you how it can become damaged, and crucially, how commensal (or ‘helpful’) bacteria and fungi play a fundamental role as foot soldiers protecting this defensive perimeter. Informed by recently published research carried out here at The Florey Institute, we also discussed how the distinction between organisms that are desirable to have on and within our bodies, and those that are not, is often far from clear, and that not all microorganisms come in peace!

With this in mind, we encouraged festivalgoers to have a go at propagating their microbiomes on pre-prepared agar plates, which we then transported back to the University of Sheffield and incubated - many of these are very beautiful and we encourage you all to check out them out at www.floreyinstitute.com/invisible-worlds-2019.html 

“Our research has shown that the ‘normal’ human microbiome can even help the opportunistic disease causing bacterium Staphylococcus aureus establish infection. The interaction between our microbiome, potentially dangerous organisms and our bodies is complex and far-reaching. It is fantastic to be able to bring it to life and show people in this way!” – Dr. Daria Shamarina

If you’ve got a passion for microbiology or if you enjoyed our activities at this event and would like to know more, check out our website, our research, and be sure to follow us on social media. If you’re really keen, you could even consider becoming a member of the Microbiology Society, who offer reduced rates for students.

The bacterium Streptococcus pyogenes is a common cause of sore throat and tonsillitis. It is also currently causing an unprecedented upsurge in scarlet fever infections in the UK. During infection, S. pyogenes can release superantigen toxins that aid the bacteria in causing disease and lead to the symptoms of scarlet fever. Superantigens work by bypassing the normal immune response to trigger an increase in the blood immune “T” cells, leading to inflammation that can be harmful to the patient. S. pyogenes can produce different combinations of different superantigen types, which may contribute to disease in slightly different 
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Florey Institute member Dr Claire Turner and colleagues Dr Mark Reglinski and Prof Shiranee Sriskandan at Imperial College London recently identified two new superantigen genes in S. pyogenes, which they termed speQ and speR.  This work was published in the Journal of Infection. 
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​Reglinski et al. identified these genes initially in the genomes of two S. pyogenes isolates originally cultured from patients back in the 1930s. After searching the genomes of over 4000 other S. pyogenes isolates, they found these genes in other strain types of S. pyogenes too. Reglinski et al. confirmed that these new superantigens function in a similar way to other superantigens. 
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On 23rd March a group of our fantastic PhD students travelled down to Abingdon to take part in Atom Science Festival (@ATOMSciFest). There were a number of activities that members of the public could take part in looking into the hidden world of microbes. These included looking at what microorganisms can grow from a human face, observing immune cells and bacteria under a microscope, learning why and how to wash their hands, and to even grow the microbes from their own hands! Below is a link where you can see the result of last-mentioned activity. If you still have the number which we gave you that day, find a picture with that number and see what wonderful microorganisms have grown! Thank you for taking part in our experiment.

https://drive.google.com/drive/folders/1EJURIDobFgaeGuPif1_tnjkkU7iAm6fA

As humans, we ‘see’ because light interacting with the surfaces around us reaches our eyes. But how do we ‘see’ when want to study objects that are so small light steers around them? - like the study of objects on a nanometric scale such as individual proteins or molecules,  far below the resolution limit imposed by the properties of light?
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One solution to this is to use an object to 'touch' or 'feel' a surface to detect  what shape it has. Basically, we ‘do Braille’!

Like Braille, the next logical sense to be used when the sense of sight is missing is the sense of touch. Unlike any other microscope, the Atomic Force Microscopy (AFM) was invented in 1980’s with this idea that if we have a ´finger´ small enough, we could be able to touch and study soft biological objects such as bacteria cells, tissues, proteins, nucleic acids, etc.

​The main advantage of this technique is that we use a nanometric tip to scan entire surfaces and obtain topography of the samples without transferring energy to the sample and hence performing no harm to biological samples. At the Florey Institute we collaborate among the Departments of Physics and Astornomy, MBB and Medical School at the Hobbs’ Lab to apply AFM to study DNA interactions with other proteins and the topography of Bacteria cells.   
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The landscape of the Bacteria Cell:
In the Hobbs’ group we are very interdisciplinary. That is why there has been a long-term collaboration between Prof. Jamie Hobbs from Physics and Prof. Simon Foster from Microbiology. Carrying out this project Laia Pasquina Lemonche, a third year PhD Cohort student is using the Atomic Force Microscope to study more in depth the topography of bacteria and the molecular organization of the cell wall from Staphylococcus aureus and Bacillus subtilis.

One of the main advantages of using this technique instead of other high resolution approaches is that we can obtain very detailed information from a single cell without the need for averaging any data. As a result, we can start answering fundamental questions about the morphology of bacteria and their behaviour but also new questions are arising from these findings. Through this, we are one step closer to better understand the host-pathogen interaction and how to treat bacterial infections effectively.

​DNA-protein interactions:
Another great application of AFM besides studying the topography of a sample, it is its ability to ‘video record’ biological reaction. For instance, DNA Polymerase, an enzyme responsible for DNA replication and repair during cell division, can be allowed to act on DNA, and consecutive AFM images of the process can be taken so as to ‘see’ the process actually happening in an environment mimicking the native cell conditions. In our lab, we are collaborating with Jon R. Sayers to use the AFM approach to understand the interaction between a DNA molecule and the Flap-endonuclease protein. Vinny Verma, a second year PhD Cohort student is using High-speed AFM to investigate this interaction to understand the conformation changes that occur during the process and how the cell manipulates the DNA using biomolecular machines.
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For AFM the prospects are many, as we’re yet to see what new advancements  AFM can do for 'high resolution' imaging and even what video-AFM can do for our understanding of cells!

​PBPs are essential enzymes used by bacteria to synthesise their cell wall and are the target of β-lactam antibiotics such as penicillin. Over time however, bacteria have formed new PBPs which resist these drugs and given rise to highly resistant strains such as MRSA.
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​Being a chemist you would think I found the first part the easiest, that is synthesising suitable fluorescent probes which could bind to PBPs, but it was far from trivial! β-lactam’s are incredibly strained molecules and as such are difficult to manipulate. They can also be liable to degradation and this limits the type of chemistry you can apply. 

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​Luckily I eventually developed a protocol to work from and was able to successfully take these probes from the bench, apply to S. aureus and actually see them binding to PBPs using microscopy!

​I have recently established a probe for using in Stochastic Optical Reconstruction Microscopy (STORM) which is something we’ve wanted for a while! This will allow crystal clear images of PBP interactions and offer an insight into their precise location during cell wall biosynthesis.
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Frank Ryan is an emeritus consultant physician with an interest in medical and scientific history. He told us the story of a strange-looking vessel (pictures below) and its role in the early production of penicillin:

​"This ceramic vessel  was given to me by Norman Heatley, one of the pioneers of the penicillin story, when I interviewed him about his life in science in 1997. It was one of the vessels in which he produced penicillin at Oxford in the early trials before commercial production."

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​"I first came into contact with Dr Heatley after I wrote a book, Tuberculosis: The Greatest Story Never Told, which detailed the history of the discovery of the cure for tuberculosis. In essence this was an integral part of the history of discovery of antibiotics and chemotherapy of infection. Dr Heatley made an important contribution to the initial production of penicillin in sufficient purity and quantity to allow the early trials of its production, safety, efficacy and potential to treat a range of different bacterial infections."