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."

​As one of the interdisciplinary PhD students within the Florey cohort I get to split my time between the Physics and MBB departments. Coming from a physics background it can be easy to overlook the work that goes on in the other departments and so for me one of the best parts about my PhD is being able to hear about research and learn techniques from both disciplines.
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​In my project I am aiming to develop antibacterial surfaces that are inspired by cicadas, who get their bacteria-killing ability from nano-scale pillars on the surface of their wings. The first part of my project is to study these wings with imaging techniques such as Atomic Force Microscopy and Scanning Electron Microscopy, to learn more about their nanoscopic features. I will then use this to design and make my own antibacterial surfaces and study how cells interact with them, in order to find out more about how these structures kill bacteria.​

​This collaboration between bacteriology and materials physics will hopefully provide a “drug-free” method of reducing the accumulation of bacteria on surfaces. This could eventually prove to be useful in a medical environment, especially in the fight against the growing issue of antimicrobial resistance.
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My name is Katherine Pline and I’m a third year PhD student in the Johnston Lab in Sheffield. I am interested in how invading pathogens and infections interact with the human immune system. I work on an infectious agent called Cryptococcus neoformans, a yeast which is inhaled into the lungs and can infect the brain.
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We have used zebrafish infections to watch how the infection progresses in each fish through time and, with help from the brilliant James Bradford and Dr Rhoda Hawkins, have used this to make a computational model of what happens in infection. This research has helped us to understand how the immune system interacts with the pathogen C. neoformans, how the yeast uses our macrophages to spread, and how our body mounts defences to stop it. Like the journeys we all face, infection here can lead to a happy ending, or can end in disaster and disease. While each person who faces a challenge, an infection, is unique, we must all fight to be victorious, and learn as much as we can in the process.

As a first year PhD student, my research journey has only just begun. I’m based in the Department of Infection, Immunity & Cardiovascular Disease (IICD) and my focus is corneal infections.

The cornea is the transparent lens that covers the surface of our eyes and it plays an essential role in eyesight.  Therefore if bacteria infect the cornea, the results can be devastating and corneal infections are still a major cause of blindness worldwide. This type of infection is a particular problem in developing countries.

One of the major issues with treating corneal infections is that bacteria attach to the cornea as ‘biofilms’. A biofilm is a complex community of bacteria, held together in a sticky extracellular matrix. Bacteria within biofilms have different characteristics to free-living bacteria and one of these characteristics is an increased resistance to antibiotics. This makes it difficult to treat corneal infections and new antimicrobials are desperately required.

With this in mind, I am trying to develop an in vitro model of the infected cornea that can be used for drug testing. If successful, my PhD journey could end with the identification of new antimicrobials that are able to beat the biofilms and help to prevent corneal blindness.

In the Corrigan lab, within the Florey Institute we focus on how bacteria, specifically methicillin resistant Staphylococcus aureus (also called MRSA), respond to and deal with stressful conditions such as starvation.

​​Bacteria like MRSA produce two molecules when stressed, collectively called (p)ppGpp, as part of the stringent response. This alters their physiology in many ways – including modulating the transcriptome, inhibiting the synthesis of ribosomes and generally slowing growth.
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My name is Yin Xin Ho and I am a 2nd year PhD student working under the supervision of Dr. Lynne Prince and Dr. Ashley Cadby. My project involves developing and using super-resolution microscopy techniques to understand neutrophil and Staphylococcus aureus interaction. Neutrophils are the most abundant white blood cells in our blood and are crucial immune defenders against ​S.aureus, a highly adaptive pathogen that causes wide range of infections. 

A typical day in medical school involves getting blood from volunteers in the morning to isolate neutrophils for my experiments. Over in BICEN, I work alongside physicists, engineers and chemists to build microscope, as well as to use the microscopes that are developed in the lab to image my samples.
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