Some sporadic insights into academia.
Science is Fascinating.
Scientists are slightly peculiar.
Here are the views of one of them.

Tuesday, 18 December 2018

What is up your nose?


We are interested in the contents of your nose, not at the level of hair, bogey and the occasional finger, but at the level of the complex microbial community that lives there and how it is associated with respiratory infection. The makeup of this community has been interrogated through sequencing (the airway microbiome) with indications that some bacterial communities may be associated with health and others with disease.

A bacterial diet

However, what the bacteria in the airways eat to survive is less well understood. One tool that may help us to characterise which biochemicals in the airways bacteria can use as food is called metabolomics. This uses liquid chromatography, to separate the biochemicals, and then mass spectrometry, to interrogate what they are. Comparing the mass spectrometry data against a curated library, we can then determine which individual biochemicals are present and their relative abundance. This tool has been used widely to investigate changes in the blood but has not been used much to interrogate the airway.

Blotting paper 2.0

The aim of our recently published study was to compare methods for sampling the airway metabolome. We looked at two standard techniques – nasal lavage (flushing a millilitre of saline through the nose and recovering whatever you can – quite a lot never comes back!) and induced sputum (getting people to breathe in an expectorant and then spit in a cup). We also used a newer technique, that had never been used for metabolomics sampling, called Synthetic Absorptive Matrix (SAM) strips. These are hi-tech blotting paper and have been used to recover other types of sample from the airways, including antibodies and cytokines. You can watch a video of their inventor having them put up his nose here. We looked at the use of these SAM strips in both the upper airway (via the nose) and the lower airway (via a bronchoscope). In the traditions of Barry Marshall (though I doubt I will get a Nobel prize for this), I volunteered to be one of the subjects for the sampling; the nasal wash, induced sputum and upper airway SAM were all fine, but having a bronchoscopy was fairly unpleasant.

It’s good to share

Having collected the samples, we then outsourced the running of the metabolomics to a company, called Metabolon in the US. This choice had mixed reviews, but I think it is ok to outsource, increasingly labs are outsourcing some of the more specialist analysis approaches – sequencing, transcriptomics, metabolomics. This makes sense in terms of time, expertise and access to equipment. Specifically in the case of metabolomics, outsourcing gave us access to a much larger curated library of samples, giving us more information from our samples, the biochemicals were also grouped into families, enabling us to interrogate the data more easily.

Sooo much data

From the point of performing the study to publishing it has been a lengthy process. In part this was due to the complexity of the dataset. We had approximately 14,000 data points – which may be small compared to some types of project, but when you are used performing focussed studies on individual mediators it was quite a step change. This was combined with a bewildering list of biochemicals, most of which we had never heard of – 1-stearoyl-2-arachidonyl-GPC anyone? In the end, through the power of the R programming platform and a very talented PhD student, we have ended up with a paper that uses a wide range of graph types, all of which aimed to compress the data into a meaningful form.

Food for the Pseuds

So what did we find? In total, 581 biochemicals were recovered from the airways belonging to a range of different families. When we compared the relative abundance of the these biochemicals between the different sampling techniques, we saw that the SAM strips gave us a much greater recovery of biochemicals than the other approaches. Since we were interested in how the airway metabolome enables bacterial colonisation, we screened some of these biochemicals for their ability to support bacterial growth. 35 of these biochemicals were able to support growth of the opportunistic airway bacteria Pseudomonas aeruginosa, including a number of sugars and amino acids.

A microcosm in a nostril

The airways represent a fascinating ecosystem because they are nutritionally more restricted in terms of the range and specific concentrations of any one biochemical compared to say the gut, but at the same time the nutrients are constantly refreshed. The balance of biochemicals in the airways shapes the bacteria that can live there, and we believe that this could be dysregulated in disease. By developing the tools to sample the airway metabolome, we are now one step closer to understanding how changes in airway biochemistry affects infection.

Tuesday, 20 November 2018

Buy one, get one free: Vaccinate the mother, protect the child


Flu vaccine the best way to protect

Infection with influenza virus, the causative agent of flu, is particularly severe in pregnant women and newborn children. If they do get infected, they are far more likely to get severe disease leading to hospitalisation. For the pregnant mother, the simplest approach to avoid this is to get the flu vaccine as soon as it becomes available. However, these vaccines are not licensed for children under 6 months of age – leading us to ask the question, how do we protect newborn children against influenza infection?

Maternal vaccination, protecting both mother and child

Luckily, the body has already come up with a solution. During pregnancy, mothers pass on immunity to their children. This passive protection is transferred in the form of antibodies, which are proteins made by the immune system that are highly specific for the molecules that make up the coats of viruses and can prevent the viruses from infecting our cells. This antibody transfer occurs in the second and third trimester of pregnancy and has evolved so that the newborn child has some early protection against whatever infections the mother has been exposed to. We can utilise this system with maternal vaccination. If we vaccinate the mother, she will make antibodies that recognise the virus in the vaccine and some of these antibodies will pass from her to her baby. This maternal immunisation approach has been seen to be very effective in reducing the burden of infection with tetanus and pertussis (whooping cough) in babies. Maternal immunisation has also been recommended as a method of reducing influenza infection in babies since 2005.

When is the best time to vaccinate?

One important question is when is the best point during pregnancy to vaccinate the mother to ensure the maximum transfer of antibody to the baby. It was originally thought that early in the third trimester (weeks 25-36 of pregnancy) was best as this was the peak of antibody transfer, but recent studies investigating pertussis vaccination of mothers saw higher levels in babies if the mothers were vaccinated in the second trimester (weeks 13-24 of pregnancy). We wanted to explore the best time to immunise mothers with influenza vaccine. In our latest paper, we measured the level of influenza virus specific antibodies in both mothers and babies at the time of birth. We compared babies born to mothers who were vaccinated in the first, second or third trimesters with babies born to unvaccinated mothers. We saw that there was significantly more influenza specific antibody in babies born to vaccinated mothers than in those born to unvaccinated mothers – demonstrating that maternal flu vaccination is highly effective at boosting the protection against influenza infection in the baby. We then investigated timing and observed that the high levels of antibody were seen in children born to mothers vaccinated in either the second or the third trimester, suggesting that either timepoint was equivalent, though there was less antibody transferred if the gap between vaccination and birth was less than four weeks.

Flu the ever changing

However, there is a complication with influenza virus; unlike the other pathogens for which maternal immunisation is recommended – pertussis and tetanus, the influenza virus changes. These changes in virus necessitate a new flu vaccine each year to match the viruses that are circulating. Flu is also seasonal – you are much more likely to get flu in winter months (in temperate climates). This seasonality had an effect on the levels of immune protection in our study: children born during the flu season had higher levels of antibody than those born outside it. 

The time is now

When we put the seasonality of influenza together with the best time to vaccinate mothers to pass antibody to children, we see that the current practice of offering flu vaccine to mothers as soon as it becomes available gives the best balance of protection to both mothers and their babies at the times when they need it most. This is because the flu season is 6 months long and pregnancy is nine months long. Whilst immunising mothers in the first trimester does not pass on the most antibody to the baby, immunising the mother at the start of the flu season gives the mother maximal protection for the whole flu season and they will give birth outside the flu season, so the baby requires less protection. Mothers who are in the second or third trimester at the start of the flu season will benefit from the protection of the vaccine themselves and pass antibody protection to their baby.

Therefore our study supports the current practice of offering influenza vaccine to mothers as soon as it becomes available.

Thursday, 30 August 2018

What are science?

Apparently we all fucking love science, or at least we love pretty pictures, anecdotal facts, chemical explosions and slightly preachy environmentalism.

However, science is none of these things. Science is the generation and testing of ideas; normally disproving them, in the process generating more ideas that need more testing.

Science junkies

Sadly, the day job of a scientist is nothing like the programs ‘Bang goes the theory/Tomorrow’s World/Johnny Ball Reveals All’ (delete as appropriate depending on your generation): in my 20 years being a professional scientist, there has been no time at work when I have blown anything up, thrown heavy weights into bowls of custard or put Mentos into bottles of Diet Coke.
To be honest, blowing things up at work is frowned upon and the management go to some lengths to prevent us blowing up the building (just another example of health and safety gone mad).
Highly visual demonstrations of chemical reactions are educational if phrased properly – if I do this, what do you think will happen and why? And these demonstrations can be effective for attracting the impressionable to a life of science. In effect, flashy chemical reactions are the gateway drug to scientific addiction.
At school we had a teacher who once a term gave us unrestricted access to the chemical store and a Bunsen burner; I imagined this was what it would be to be a scientist. Nowadays I don’t even get to do experiments, and yet I identify more as a scientist now than when I was doing my PhD as a space-filler before getting a “real job”.

Indoor work, no heavy lifting

So if the day-to-day of science isn’t setting things on fire, what is it?
It is immensely varied, and depends upon both the stage of your scientific career and the field you work in. But the main work of science is testing ideas. Some of which involves being in a lab, but most of which involves sitting in an office analysing the results from your experiments or coming up with new ideas because your experiments haven’t turned out as expected.
Since 99% of these ideas come from other people, another major strand is evaluating other people’s ideas and building on the back of them. And since other people need to evaluate the ideas we have, we need to be able to effectively communicate them, as written articles (papers), as sales pitches (grants) or in person (conferences).
So disappointingly, the day to day work of science is not so far removed from other professions, though we do get to wear a white coat occasionally. You need to be able to read, to write and, terrifyingly, interact with other people – very much none of the things that got most of us into science in the first place.

Friday, 25 May 2018

Flu and our poo


There are various outlandish estimates about the numbers of bacterial cells there are on your body compared to the number of your own cells. Wikipedia informs me that current guestimates put it at a 10:1 ratio, with approximately 100 trillion bacterial cells per adult human; which is the kind of number that a stressed scientist makes up when the answer “I don’t know but it’s feckin’ loads” won’t suffice. Our guts are particularly rich in bacteria, and it is estimated that 30% of every poo is dead bacteria. We don’t really know for certain what all these bacteria do, quite a lot of them are probably just along for the ride living off dead skin cells and sweat. But there is a small proportion of these bacteria that we rely upon for all kinds of useful things, like breaking down our food properly, training our immune system and fighting off the bacteria that make us sick. Finally there is another group of bacteria that are just waiting in the wings to cause infection, often pouncing when we are at stressed or tired.
Collectively the bacteria that live on or in us are referred to as the microbiota and the ecological communities that they make up are called the microbiome. Our knowledge of this superficial (using its proper meaning of at the surface) second life has exploded in the last decade, mainly because of our ability to read DNA cheaply and easily. There has been a huge number of studies that have reported a link between our bacterial fellow travellers and a huge range of body functions. Some of which make some sense as the bacteria at least live at the same site as the disease including obesity, diabetes, asthma and tooth decay and some that require a more conceptual leap including mental health and autoimmunity. These links have also led to some outlandish ideas for new therapies, including faecal transplant (which is almost precisely what it sounds like) to reduce gut bacterial infection and ‘vaginal seeding’ of C-section babies.
Now that I have mentioned the obligatory facts about the microbiome – it outnumbers us, it has something to do with health and people are utilising it for weird therapies – I can concentrate on what we did in our recent paper. Given the myriad associations between the microbiota and health/ disease it is important to understand what shapes these bacterial communities. In particular we wanted to know if infection at one site, the lung, would change the bacteria at another, the gut. We looked at two important respiratory pathogens, respiratory syncytial virus (RSV) and influenza. Following lung infection, we observed a transient but significant change in the bacteria present in the guts.
One of the offshoots of studying the microbiome is that you need to learn (or relearn) your Linnean classifications (which for those of you that can’t remember go Domain-Kingdom-Phylum-Order-Family-Genus-Species: so for example humans are Animals-Chordates-Mammals-Primates-Hominids-Homo-Homo sapiens). We saw a shift in the bacterial phyla with a big decrease in the Firmicutes phyla and an increase in the Bacteroidetes phyla. Further subdividing within these phyla we saw a decrease in the Lactobacillaceae family and an increase in the Bacteroidaceae family. More strikingly, when we analysed at an approximation to the species level, we saw different species profiles with each experimental repeat. This suggested that lung infection wasn’t specifically affecting one or two species, rather it was changing the gut environment in such a way that one phyla of bacteria (the Bacteroidetes) would benefit at the cost of another (the Firmicutes). This change was acute and transient and by the time the mice had recovered from infection, their microbiome had also recovered.
Like most of science, this study acts as a starting point, asking more questions than it answers. What does it all mean? Frankly your guess is as good as ours. There is some suggestion that Lactobacillus are ‘good bacteria’, mostly from Yoghurt manufacturers who are trying to claim that a fruity, milk-based pudding is in some way good for you. One speculation is that if the bugs in our gut produce things we need to be healthy, lung infection, by disrupting the gut microbiome, may amplify sickness. But we would need to replace the ‘good’ Firmicutes and see an improvement of disease outcome to demonstrate this. Why is this happening? Again, we don’t have an answer. We had one tantalising result, which was that there was an increase in proteins associated with airway mucus in the guts, which occurred at the peak of point of bacterial change. Many of the bacteria in the Bacteroidetes phyla can utilise mucus as an energy source and so the swallowed mucus may support their growth. As I type, we are following up on both of these questions – so stay tuned and we might just have the answers, or more likely more questions!