A step-change in computer power for aspergillosis genomics

Quantum supremacy

Future research in aspergillosis genetics will be (and is being) done with huge computers as they analyse entire genomes and generate huge amounts of data from the information gleaned when sequencing robots read entire genomes of complex living organisms – Aspergillus or human. The human genome contains about 3 billion base pair letters that together form a complex collection of 20-25,000 genes.

Each of these genes may be switched on or off in an infinite array of gene expression that not only makes an organism what it is but also regulates the response of a human body to external events such as infection. It is likely that mistakes in how some of these genes are expressed or how they function contribute to the reason why some of us are vulnerable to fungal infections such as aspergillosis while most of us aren’t.

Working out which of this huge number of genes is responsible for allowing fungal infection is clearly a massive task, but it is more complicated than that. If we were to sequence the genome of one person we would only get very limited information about which of their genes are fungal infection susceptibility genes. Perhaps there is more than one gene involved? As a consequence, we need to sequence the genomes of many more people who have aspergillosis in order to get a more accurate impression of the number of genes involved, and which genes are involved in permitting a fungal infection.

We also have to sequence the genomes of people who haven’t got aspergillosis so that we have something to compare the test subjects with. All in all, we will need to sequence dozens of individuals in order to arrive at reliable conclusions. This takes many months to achieve.

Computer power

Even with our most powerful computers at the University of Manchester this still takes a lot of time. Investment in Edinburgh genomic computing resources uses state of the art computer power that is 5 x faster than its predecessor, but this is just a linear progression rather than a dramatic step-change in performance likely to radically speed up the genomics work.

Additionally, however fast these computers already are, the rate of advance in computing speed will be forced to slow down as current technology will soon reach its fundamental limits – for example current computers work with ‘bits’ that represent two states – I and O so we have lots and lots of power but only the ability to work with ‘yes’ or ‘no’. This isn’t enough to process the forthcoming mass of incoming data – we need a complete step-change in how computers work to achieve fundamental accelerations in speed.

Google and quantum bits

Google, apart from being a huge company that provided services to you and I, is also a computer research company. It has been working on this fundamental limit to computer speed for some time and has just announced the successful construction of a computer that uses quantum particles rather than ‘bits’. Quantum bits can work with many more states compared with ‘bits’ so you can imagine how that might speed things up a little. Instead of ‘yes’ or ‘no’, each particle can also store ‘maybe’, ‘yes and no’ and many more – each of these new states would have taken many current bits to achieve the same end.

We can only really appreciate the huge improvement in speed this offers by setting this new computer a really difficult problem to solve – one we know will take a computer using current technology a long time to finish. Google claims that when they set a current computer a particular test problem it would take 10,000 years for it to solve it – I presume that they haven’t actually tested that using a realtime run!

Quantum supremacy


How long did the computer using quantum bits take to work out the same problem? It would be really amazing if it could do it in 100 years, incredible if it could do it in 10 years. In fact, Google claims it took just 200 seconds – truly a step-change in computer power for aspergillosis genomics.
If we are able to use that kind of computer power for genomics work in the future we would have results in fractions of a second, speeding up work on aspergillosis genomics 1000’s of times, making it theoretically possible we could be doing complete genome checks in a single visit to the clinic in the future.

https://www.bbc.co.uk/news/science-environment-50154993

Stoptober

Stoptober is an initiative which aims to help people quit smoking. The dangers of smoking are well understood, but for those with chronic lung conditions the risks can be even greater – for example smokers are 5 times more likely to catch the flu, a major complication for aspergillosis patients.

We have had 2 talks at the National Aspergillosis Centre patient and carer support meeting that mentioned smoking and aspergillosis. At one meeting, Dr Khaled Al-shair (National Aspergillosis Centre Researcher) spoke of several guidelines to help patients suffering from Chronic Pulmonary Aspergillosis (CPA) feel their best while being treated at the NAC. Exercise and good diet played their part but one of the major improvements many patients can make to their lifestyle was to stop smoking cigarettes.

We have also had a talk from our local ‘Stop Smoking’ nurse – this talk focused what can be done locally using UHSM (University Hospital of South Manchester) services; so if you are a NAC patient or live withing striking distance of UHSM (Manchester, UK) you can take advantage of this help directly. There was also extensive information for anyone about the advantages of giving up cigarettes and different strategies to employ when trying to find a way to stop smoking.

The NHS also provides a wealth of information and advice on quitting smoking which can be found here.

Advice for people with respiratory conditions in winter

Many patients with respiratory conditions like aspergillosis report increased frequency of chest infections during the winter months, and this is mentioned repeatedly in our Facebook support groups (Public, Private). The cold weather brings problems of many kinds, but respiratory infection is one of the most serious. Infections by bacteria or virus have a major impact on their quality of life as their breathing becomes restricted and often they quickly become too exhausted to carry on with tasks of daily living.

Why does the winter cause increased vulnerability to respiratory infections? Is it because of the cold weather making us weaker and unable to fight off infection? In part – yes it is! Cold air cannot hold moisture as well as warmer air and thus cold air, is drier air. Inhaling dry air tends to dry out our airways and this can make us vulnerable to infection. This has two impacts – it irritates the lining of our airways and makes us cough, which itself increases our risk of infection, but it also dries out the mucous lining our airways and makes it more difficult to move – so we end up coughing much more than normal as we try to cough up this thickened substance.

People with chronic respiratory disease such as COPD, asthma, aspergillosis are particularly vulnerable to dry air as their airways are very sensitive to irritation.

Winter holds all kinds of pressures for the NHS and one of the biggest is a huge increase in people with respiratory conditions whose condition has become worse as a result of the cold weather. This video includes some advice on how to make sure the cold doesn’t affect your condition to prevent you from needing hospital treatment.

Reproduced with thanks, produced by NHS Blackpool CCG 2019

We Are Undefeatable

We Are Undefeatable is a campaign which aims to help those with chronic health conditions exercise. Both the conditions and forms of exercise vary widely – the goal is to find out what works best for you!

Visit the website to discover how exercise has helped other people with chronic conditions, and what the campaign can do for you : We Are Undefeatable

For more information on exercises specific to aspergillosis and chronic lung conditions:

World Mental Health Day 2019

#AudibleSessions#WorldMentalHealthDay#AndThatsOkay

As part of World Mental Health Day 2018, nine celebrities spoke about their experiences of mental health problems, from what their depression feels like to the things that have helped them. Featuring Susan Calman, Clarke Carlisle, Marverine Cole, Bryony Gordon, Matt Haig, Matt Johnson, Katie Piper, Vicky Vox and Simon Webbe.

For more information:

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