Spores: Extreme Survivors

Written by Lucy Eland, Edited by Nicola Simcock

Have you heard about the 40 million-year-old bacteria that survived inside the abdomen of a bee, preserved in a chunk of amber? Amazingly, when removed from their amber tomb and given nutrients, the bacteria were still able to grow! Our speaker this month, postgraduate researcher, Clare Willis, from Newcastle University’s Centre for Bacterial Cell Biology, explained how this is possible.

When conditions become extreme, some bacteria create an ‘escape capsule’ that allows them to survive in an inactive state, until the environment becomes more favourable. This ‘escape capsule’ is known as a spore and contains all the bacteria’s genetic material packaged up into a hardy capsule, that protects it from damage. Clare explained to the captivated audience that this spore state can be problematic for humans. Many bacteria, known for their antibiotic resistance in hospitals, such as Clostridium difficile, can make spores that are difficult to destroy. Anthrax infections and botulism are also caused by spore-forming bacteria. These spores can lie dormant and undetected, before flaring up rapidly and causing serious infections.

Making a spore

Infographic showing how a spore forms within a bacterial cell once the bacterial DNA has been duplicated. 

Clare’s research for her PhD looked at how spores are created, which could offer valuable insights into how spore-forming bacteria can be controlled. Under normal replication conditions bacterial cells split in half to make two copies, each containing one complete set of DNA. When the environment becomes uninhabitable and a bacterial cell ‘decides’ to make a spore, the DNA is copied as usual, but the cell separates into a smaller cell (‘prespore’) and a larger one (the ‘mother cell’). This means that one copy of the DNA must move across the dividing cell into the prespore. Clare’s work looked at how this happens ─ with the aid of fluorescent tags stuck onto the DNA. These tags allowed her to study the movement of the DNA with a microscope, by tracking the fluorescent colours. Once she tagged the DNA she found something surprising ─ both DNA copies moved towards the prespore, not just one. This led her to think that the two DNA copies must be attached together in some way. Clare carefully considered and assessed four different ways the DNA could be connected. Her favourite theory, most supported by the evidence, is that the two copies of DNA are held together by proteins. Clare hopes to do further work to find out more about these proteins and thus better understand how spores form.

Spore formation microscopy

Fluorescence microscopy pictures by Clare Willis and a supporting diagram to show how both copies of DNA within a bacterial cell move together toward the ‘prespore’ when packaging DNA into a spore. A particular region on the DNA is labelled in red and the outside of the cell is labelled in green. Each picture is taken 15 minutes apart.

After recharging our glasses, there was much discussion and lots of questions from the audience:

What happens to the mother cell after the spore is formed? It bursts and dies!

How long does it take to make a spore? Longer than normal cell division, as the spore needs to be coated in proteins before it can emerge from the mother cell, usually a few hours.

Do all bacteria in a community make the same ‘decision’ about when to make a spore? A population of spore-forming bacteria will differ in the timing of spore production, depending on how each cell senses and responds to environmental changes.

And how long does it take a spore to ‘germinate’ and start growing again? Depending on the species, bacteria can emerge from the spore within hours of exposure to a suitable environment and nutrients.

Clare’s excellent talk gave us all a great introduction to the wonderful, microscopic world of bacteria and one of their most extreme survival mechanisms.

We look forward to seeing you at the next SciBar event on Wednesday 21st of November where we will hear Riona Mc Ardle’s talk ‘What can walking tell us about dementia?




Battling the bugs: Microbiology and the NHS

Words by Nicola Simcock, Edited by Joe Crutwell

For this month’s SciBar we were taken on a microbiology rollercoaster; from the highs of an ‘outstanding’ care quality commission assessment, to the lows of the Bristol stool chart. Angela Geering ─ a Training officer and Advanced Biomedical Scientist ─ talked us through her experiences as a Blood culture section lead at the Freeman hospital.

Rosy-cheeked from the warm weather, the crowd at The Old George soon learned the impact of the sunny season on hospital infection rates. The lure of an open-toed sandal leads people to finally confront those discoloured toenails and cases of athlete’s foot skyrocket. As BBQs are fired-up, hungry people take their chances with undercooked chicken, meaning Salmonella diagnoses become commonplace.  However, as the worrying list of bacteria grew, Angela reminded us how these invaders are rapidly diagnosed and treated within our beloved NHS.

Integrated laboratory medicine ─ testing and treating medical samples in hospital laboratories ─ provides 70% of diagnoses. Everything can be screened for infection; from ‘standard’ samples like blood, stool and urine, up to transplant organs, heart valves and solid joints. Even swabbing the inside of a detached finger is not beyond Angela’s expertise. Such examples, and many more, all contribute to the 1 million samples that are processed through the Newcastle facility every year.

Impressively, Angela and her team can identify a positive blood culture within 30 minutes. Some bacterial classification involves spreading blood cultures on agar ─ a jelly-like substance enriched with different nutrients. When stored at an appropriate temperature, nutrient-rich agar promotes rapid bacterial growth. Special compounds can be added to the agar to help identification. For example, E. coli (Escherichia coli) ─ a major culprit for urinary tract infections (UTIs) ─ will appear pink on the appropriate agar. Once grown, the size and shape of a bacterium may also reveal its identity, and microscopy is used to locate clusters, pairs, rods or chains. Angela notes that many routine lab tests are still manual – requiring an actual scientist to run the test and/or analyse the results. However, with improving technology, an increasing number of tests are becoming automated to reduce labour, time and cost of analysis.

Caption: The friendly ‘face’ of Giardia lamblia – a common faecal parasite. Transferred through infected water or food, it colonizes and reproduces in the small intestine causing diarrhoea and abdominal pain.


It’s unsurprising that work as a biomedical scientist can sometimes get a little smelly, but this doesn’t deter the team from “putting patients at the heart of everything we do”. This became clear as Angela described the network in place to ensure efficient transfer of medically relevant information. Following sample analysis, the team work closely with consultant microbiologists and medical staff to advise on treatment options. From receiving samples, right through to treatment, experts in every step of the process contribute to a positive patient outcome.

Understandably, speed of diagnosis is important, especially if there is an unknown outbreak on a ward. One bacteria high on the NHS ‘watch-list’ is Clostridium difficile, also known as C. difficile or C. diff. C. diff was named for being notoriously ‘difficult’ to grow and study in the lab. Infections usually occur following antibiotic-use that degrade the existing ‘good’ bacteria in the gut. C.diff symptoms include diarrhoea and stomach cramps, however, if untreated, the infection can become much more serious. An outbreak of C. difficile is so tricky to contain that hospitals operate strict patient-care procedures, equipment cleaning methods, and there is even a financial incentive to prevent its spread. Only 76 cases of C. difficile are allowed per calendar year, with each additional case costing a hospital £10,000.

With hospital-outbreak horror stories vivid in the mind, this was a main source for questions from our crowd. We learnt that MRSA (Methicillin-resistant Staphylococcus aureus) ─ a familiar villain of newspaper headlines ─ is now considered ‘old-school’ in microbiology circles, with an NHS target of zero cases for 2018/19. There is however, a new bacterium to keep our biomedical scientists busy: Carbapenemase-producing Enterobacteriaceae, or CPE for short. CPE cases are increasingly detected in UK labs and worryingly, are showing signs of multi-drug resistance.

Currently, antibiotic resistance is as high on the international public health register as terrorism. While alarming, we can take some comfort in the fact that the risks of this threat are being taken seriously. Angela also helped to stem our fears with the news that; while resistance is a problem, her team are yet to face a patient they couldn’t treat. Alongside their dedicated work in the lab, members of the team additionally scan the medical literature to predict what beastly bacteria may be next to infect the North East. The team are up to date on the threats and well-prepared for how to deal with them. So, try not to worry, it seems we’re in good hands!

Waste not want not: Wastewater wattage!

Words by Joe Crutwell, Edited by Nicola Simcock

This month’s SciBar was presented by Dr Elizabeth Heidrich, an environmental engineer from Newcastle University. The subject was something that travels below our feet every day, produced by everyone without a second thought: wastewater.

The crowd in the Old George was notably reserved when asked to name what made up wastewater, perhaps out of politeness. Dr Heidrich quickly convinced us why this flow ─ that many of us think of as merely sewage ─ could be much more than a reason to turn your nose up, and even one of our most neglected resources.

Wastewater does not solely emanate from our bathrooms, it also includes excess rainwater, and the run-off from production facilities such as factories. These components mix together in our sewer systems, with a varying balance of water, oxygen content and microbiology. Sewage often has much higher levels of microbes and lower levels of oxygen that what is in our rivers and seas. To fix this imbalance and avoid causing damage to our waterways, this flow must first go through a water treatment facility.

Water treatment facilities process wastewater so it is safe enough to return to the ocean. They are not, as Dr Heidrich explained, used to produce drinkable water. Wastewater is classed as unsafe if there are too many bacteria or too little oxygen. Such imbalances will damage subsequent ecosystems, creating a toxic environment for the animals and plants that live there, making water treatment a very important process.

Treatment facilities have two main methods to create safe water: trickling filters and activated sludge. Trickling filters work by spraying the wastewater onto gravel. The trickling filter gravel is covered in a film of bacteria, and the bacteria and gravel are carefully maintained to ensure they increase the oxygen level to the correct amount by eating the biological matter found in the wastewater. Alternatively, the activated sludge process works by collecting wastewater in huge tanks, into which oxygen and sewage-digesting bacteria are injected. Once digested, the sludge settles on the bottom of the tank and the resulting treated water is drained from the top. While effective, both processes require a lot of space, and importantly, are very expensive to power.


In the UK, this process costs 1-2% of GDP, which could be reduced with increased efficiency. However, for less developed countries these costs are unmanageable, which leads to over 80% of untreated wastewater returning to rivers, severely increasing the risk of disease and contamination.

The big problem is technology. Over the last 80 years we’ve seen phones become supercomputers and wooden planes advance to supersonic machines, but sludge tank technology has not changed.

Dr Heidrich asks, is the science just not sexy enough?

Luckily, she has devised an ingenious solution to this problem, and it relies on one simple fact: the energy to power water treatment is locked within the wastewater itself, over ten times over!  The bacteria and microbes stored in the water could potentially be used to generate power, requiring only a battery to store the harvested energy. It could allow countries like the UK to ‘break even’ on water treatment, and provide solutions to less energy-rich countries by making wastewater an energy source, rather than an energy sink.

In a world first, Dr Heidrich and her lab managed to create a battery that harnessed the energy locked in the wastewater, the same way chemical energy is locked in coal or oil. But instead of combustion, this energy is obtained through using specific bacteria. These bacteria digest wastewater, using it as fuel. These bacteria then act like ‘wires’ within the battery, producing an electric current. Whilst still in the prototype stage, the potential of this technology ─ if the battery can be scaled up from lab-use to commercial range ─ is monumental.

Issues still remain however, such as the need to keep the various battery parts clean, whilst maintaining functionality in the many different water treatment centres and types of water around the world. For instance, the fat content of water is an issue known to affect the efficiency of this process.

After fielding many questions, the Old George agreed that far from being a waste, Dr Heidrich has treated us to an enlightening talk on a very important topic for our future.

If you want to attend the next SciBar, please keep an eye on the upcoming events page.

Colour-blindness- It’s not just black and white

Words by Lucy Eland, Edited by Calum Kirk

SciBar on the 21st of March saw BSA volunteer and science writer, Joe Crutwell entertain a packed room with his personal and research experience of Colour-blindness. Joe has more than mere scientific curiosity for the topic, having been diagnosed with red-green colour-blindness at the age of 10. He later had the opportunity to study the condition from a genetic and neuroscience perspective, during his undergraduate and master’s degrees.

Three proteins, collectively called opsins are needed for people to be able to differentiate colours. The instructions for the proteins are found on the sex chromosomes. The position of the instructions mean that the condition occurs far more often in men than in women. Joe went onto explain the different types of colour-blindness and their genetic causes. These range from mild forms of red-green colour-blindness all the way to seeing only in black and white.

Joe led us through his personal journey. It was interesting to hear how colour-blindness is tested for, using Ishihara diagrams (see below). And how the stigma attached to people with colour-blindness in countries like Japan is such that people spend hours learning how to cheat the tests, so as not to be diagnosed. In the UK there are few restrictions on the occupations of people with the conditions, except being in the armed forces or being an electrician. Joe led us through the fascinating world of accidents throughout history that have been blamed on colour-blindness, including a train crash in 1875 and many people jumping traffic lights! These kinds of cases have resulted in a number of countries not allowing people to drive if they are colour-blind.

Ishihara Test

Can you spot the number?

The latest research in colour-blindness has focused on curing or improving the colour vision of those with the condition. Joe was given the opportunity to try on a pair of colour correcting glasses by a scientist running a study at Newcastle University. The study will look at how effective the glasses are, and researchers are currently recruiting colour-blind volunteers. Joe gave us a great insight into the psychology of whether trying on the glasses could actually make the person with colour-blindness feel worse about having the condition, after all it is hard to miss something you have never experienced. The prospect of trying them on raised questions such as ‘Is trying them on going to ruin my life? Will everything seem really dull when I take them off? Despite his reservations Joe plunged in and found that for him, though they made everything brighter and cleared, the effect soon wore off. The suggestion so far has been that while they improve colour perception, they don’t actually make people able to pass the Ishihara test, however we will have to keep an eye on Joe’s blog to find out about the results of the current study!

After having a breather and recharging our beer glasses, Joe fielded lots of questions covering all aspects of the condition, from what it is like to have it as a child when you don’t really know what other people are seeing to how we could use gene editing methods to cure the condition in the future.

Join us for our next SciBar event on the 25th April, where Dr Elizabeth Heidrich, will be telling us about her research on how we can get energy from our waste.

If you or one of your relatives is colourblind and living in the North-East area, contact Cat Pattie at C.E.Pattie1@newcastle.ac.uk or @C_Pattie1 on Twitter if you would like to help further research into the condition.

Joe’s blog can be found at inacrutshell.com

Epilepsy Drugs and Pregnancy: A Doctor’s Dilemma?

Words by Joe Crutwell, Edited by Calum Kirk

Our November SciBar was presented by Dr Rhys Thomas. An epilepsy researcher and honorary consultant. Dr Rhys put the SciBar patrons in the position of a clinician, allowing us to see the difficult balance that must be struck while making decisions for a patient.

Classifying epilepsy, which affects approximately 1% of people in the UK, is not easy. It is a chronic condition, but it’s symptoms are intermittent and can be severe. It is a brain disorder, but can manifest at any age. It has underlying genetic triggers but an environmental correlation has been shown with factors such as economic deprivation.

Despite this knowledge, the exact causes of epilepsy are not known, but this has not stopped many treatments being discovered that help alleviate the seizures that are the main symptom associated with the disease.

Nov SciBar 2 cropped


One of these treatments, which has been used in epilepsy treatment since the 1960s , is sodium valproate . It is unclear how the treatment works as it was discovered, like many early drugs, by accident. It has a documented history of being able to halt the occurrence of seizures whilst having a relatively low rate of side effects, with one very important and very worrying exception.

After researching records of valproate use in pregnant women, it was discovered that there seemed to be a significantly higher risk of birth  defects, including intellectual defects, if a woman is on valproate during her pregnancy.

Despite these findings being quickly incorporated into advice given by medical professionals, as of 2017 almost one-fifth (18%) of women taking sodium valproate didn’t know the risks this medicine can pose during  .

These worrying side-effects coupled with the lack of patient awareness led to sodium valproate being prominently and negatively featured in the media, with some publications referring to the drug as “worse than thalidomide .”

There is another side to the story of Valproate however. Being the most effective epilepsy drug, any deviation from this treatment increases the risk of seizures. Epilepsy causes a high number of deaths in pregnancy. So despite valproate being worse in pregnancy, in men and non-pregnant women it is by far the drug of choice .

After describing all of the up to date information outlined above, Dr Rhys then left it up to the audience of the SciBar as to what they would prescribe for an epileptic patient who has become pregnant and is already on valproate. Was the right decision to keep the person on the drug, risking potential abnormalities, or change them to another, increasing the risk of a seizure?

After much discussion, the audience agreed there was not always a ‘right’ answer in these situations, especially as you cannot know the outcome until after the decision has been made. This is why current methods in medical practice involve patient-shared decision making. The patient is given all the resources possible to understand the potential benefits and risks of the treatment, and able to take a part of that important life decision into their own hands.

This was the British Science Association’s last SciBar of 2017, thanks for everyone who attended and made the events as popular as they are. If you missed us, keep an eye out on our Facebook and Twitter for what events we have coming up in the New Year!

For current UK advice about epilepsy and pregnancy follow this link: www.nhs.uk/Conditions/pregnancy-and-baby/pages/epilepsy-pregnant.aspx


Star waves and hue’s Clues: What can light and radio signals tell us about outer space?

Words by Joe Crutwell, Edited by Lucy Eland

At this month’s SciBar, we were treated to a talk by Dr Nick Walker, a lecturer and researcher at Newcastle University. Dr Walker specialises in both astrochemistry (studying the chemical make-up of outer space) and spectroscopy (the study of the interaction between matter and electromagnetic radiation). While these may both sound like quite “out-there” topics in their own different ways, Dr Walker brought everything back to earth with an in-house (or rather ‘in-pub’) demonstration.

Recreating an experiment from 400 years ago, Nick showed us how you can split light into a spectrum of colours using nothing more than a camera and an intense light source. For the work Dr Walker discussed, this intense light source was stars.

In the early 1900’s the director of Harvard Observatory, Charles Pickering, hired a group of women to process astronomical data relating to the spectrum of stars. This data helped create the “Hertzsprung-Russell” diagram, pictured below, that charts stars on a scatter plot based on their temperature and visible light wavelength.


It is possible to learn something about the chemical makeup of an object by studying the colour of light it emits. Nick described how scientists in the 1800’s worked out the chemical makeup of the sun by looking at the wavelengths of the colours it does not emit. This process was extended to other stars to give us a stellar fingerprint of our surrounding space.

This act of breaking up and studying visible light can be performed on other parts of the electromagnetic spectrum, from extremely fast gamma waves to slower radio waves. Radio waves are detected by installations such as the Atacama Large Millimeter Array in Chile, as radio waves are able to permeate through earth’s atmosphere.

These radio telescopes are capable of detecting specific molecules in space. As such, the desire in the scientific community has been to try and detect the presence of organic molecules in space. These molecules are known to be a precursor to life, and may help us answer one of science’s great questions. Did the building blocks of life come into being on earth, or did they land from outer space?

These questions are still to be answered, but spectroscopy is on the case. Telescopes looking at the infra-red spectrum can tell us about stellar dust, the molecules that make up stars. Dr Walker stated that this dust may help us understand where all this complex chemistry originates. Various probes have been sent into space to examine this cosmic dust, including the Cassini probe, which recently was sent crashing into Saturn at the end of it’s twenty year mission.

The next SciBar will be examining one of the most complex products of this sophisticated organic chemistry, our brains! More specifically, Dr Rhys Thomas from Newcastle University’s Institute of Neuroscience will be giving a talk on epilepsy and pregnancy. Join us on the 29th of November!

Genes, stats and rats – with juggling, songs and raps

Words by Lucy Eland, Edited by Joe Crutwell

This month’s SciBar saw Dr Lynsey Hall explain her research on the genetic basis of depression, through the medium of comedy!

Lynsey, a statistical geneticist from Newcastle University’s Institute of Genetic Medicine, explained the types of genetic variation that can occur using juggling and references to Mickey Mouse’s uncontrollable broom production spell from Disney’s Fantasia (a stop gain mutation!).

During her PhD research, she hoped to detect the genes responsible for depression using a Genome Wide Association study, or GWAS. This technique takes the genetic data from people both with and without depression, and does a huge ‘spot the difference’ between the two. Though according to Lynsey, doing a GWAS for depression is more like a misprinted ‘Where’s Wally’ with no Wally! After a frustrating period she did a statistical power calculation and realised that the chances of finding genes for depression are extremely small. This is because depression is both very common and difficult to quantify, with symptoms varying widely between different people. Another difficulty is that for the current methods people are only divided into ‘depressed’ or ‘healthy’ groups, and depression is just not that black and white.

The difficulties with statistical power and the need for experiments that can test possible drugs on rats led Lynsey to look for other ways to measure depression. The test that Lynsey guided us through was a rat cognitive bias test. To put it simply, rats are put in a maze of sandpaper-lined tubes and sand-pits. The sand-pits contain either a cheerio and a tube of smooth sandpaper or chocolate and a tube of rough sandpaper. The rats were then trained up to make sure that they knew how to find their favourite treat (chocolate, obviously!). Researchers replaced some of the sandpaper with one of medium roughness, and used this as a measure of how optimistic the rats were. Do the rats go for the tubes with the medium roughness sandpaper in the hope that there is chocolate? It turns out that depressed rats assume that the medium roughness paper will just lead to another cheerio, and the happier rats dare to hope for more chocolate. Endless days of running rats through mazes during her PhD led Lynsey to write ‘Bowl digger’ to the tune of ‘Gold Digger’ about one of her rats, which she performed for us to much applause.

Discussion of the prevalence of depression and mental health problems amongst researchers in universities, a hot news topic at the moment, drew the talk to a close. The trials, tribulations and pains of carrying out scientific research to get a PhD were summed up perfectly in Lynsey’s final song for the evening ‘Friday I make graphs!’ (to the tune of The Cure’s, ‘Friday I’m in love’)

A lively discussion followed about the difficulties of categorising and measuring depression, how rates of depression vary between men and women, as well as whether all rats prefer chocolate to Cheerios.

You can keep your eyes peeled for the next Scibar event on the BSA facebook page. In the meantime you can give Lynsey’s past comedy sets from Bright Club on Youtube a watch, to get a flavour of what we were treated to this week.