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

Tuesday, 22 January 2019

Natural antivirals


Before the immune system is activated, cells have their own intrinsic defence against viral infection. This comes in the form of proteins that can inhibit various stages of the viral life cycle. Some of these proteins are constitutively expressed and others are inducible – activated by signals from other infected cells as part of the early response to infection. Many of the proteins that provide this cell intrinsic immunity are expressed in response to signalling by a family of cytokines called interferons, in particular interferons alpha, beta and lambda. These antiviral genes are collectively known as interferon stimulated genes (ISGs). There are a large number of these genes (upwards of 300), but knowledge of what viruses they restrict and how they do it is limited, many genes have unknown functions.

In our recently published study we investigated the role of a specific ISG called IFITM1 (short for interferon induced transmembrane protein 1). IFITM1 is one of 3 IFITM proteins expressed by human cells and they appear to have a role in restricting early events in viral ifnection. We followed up previously published work, investigating where in the cell the protein was expressed and showed that unlike the better characterised IFITM3, IFITM1 was found on the plasma membrane, suggesting it prevents direct viral entry. We demonstrated that for a wide range of RNA viruses that infect the respiratory tract, including Respiratory Syncytial Virus, Influenza and Measles, increasing the level of IFITM1 in the cell reduced the level of viral infection. Interestingly we showed that IFITM1 was able to prevent infection with a virus with a DNA genome (Herpes Simplex Virus), suggesting IFITM1 function was associated with its cellular location rather than an effect on specific viral families. The importance of the location of the protein with in the cell was supported by studies that reduced the ability of IFITM1 to localise to the cell surface, leading to increased infection. These studies were supported by increased levels of infection in mice lacking the IFITM1 gene.

Understanding more about the function of interferon stimulated genes can help us to understand how viruses infect cells and may provide insight into strategies to prevent viral infections. In the case of IFITM1, we have shown that human cells make a robust anti-viral response at the cell surface and this can help to reduce viral infections.

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.