July 2016 – The Brain Bank North West

Why do astrophotographers spend all night under the stars?

July 30, 2016 by The Brain Bank North West

It’s a sensible question. You may think that our love of the celestial domain keeps astrophotographers up all night, or maybe it’s because there are so many astronomical targets out there that it takes all night to photograph them. Or maybe because our telescopes are so complicated and delicate it takes us hours to set them up. Well these points may partly explain why I frequently keep my wife awake as I struggle to move my telescope back into the house…often past 4:00am! But there is a deeper reason; one that means almost every astronomical photo you see probably took hours or days of photography to produce. In this post I shall explain, with examples, why I and other poor souls go through this hassle.

Let me begin by saying that during a single night (comprising maybe 4-6 hours of photography time), I certainly do not spend my time sweeping across the night sky snapping hundreds of objects. Instead, I usually concentrate on photographing 1 or 2 astronomical targets – taking more than 40 identical shots of each. In this regard, astrophotography is quite different from other forms of photography. But why do this, what is the benefit of taking so many identical shots? Well, unlike most subjects in front of a camera, astronomical targets are dim…very dim. Many are so dim they are invisible in the camera’s viewfinder. To collect the light from these objects (galaxies, nebulae, star clusters…etc.) you must expose the camera sensor for several minutes per photo, instead of fractions of a second as you would for daytime photography. Unfortunately, when you do this, the resulting image does not look very spectacular – it’s badly contaminated with noise.

Two images taken as 3-minute single exposures, noise is prevalent in both. Details such as the edges of the nebulae and faint stars cannot be seen. D Elijah.

These are 3-minute exposures of the Crescent and Dumbbell nebula in the constellations Cygnus and Vulpecula respectively. You can see the nebulae but there is also plenty of noise obscuring faint detail. This noise comes from different sources. The most prevalent being the random way photons strike the camera’s sensor – rather like catching rain drops in a cupped hand, you cannot be sure exactly how many photons or rain drops will be caught at any one time. A second source of noise comes from the fact that a camera does not perfectly read values from its sensor; some pixels will be brighter or dimmer as a result. Finally, a sensor’s pixels measure light within a limited range of values. If the actual value of light intensity for a given pixel is between two of these values then there will be an error in the reading. There are further types of noise in astronomical images such as skyglow, light pollution and thermal noise but these can be dealt with by calibrating the images – a rather complex process I will discuss in a future post!

By stacking multiple images, noise is reduced and the signal, like faint stars and subtle regions of nebulae, become more apparent. Photo sourced from www.dslr-astrophotography.com.

The best way of dealing with this noise is to take many repeated exposures and combine (stack) them. This method takes advantage of the fact that each photo will differ because of the random noise they contain but critically they will all contain some amount of signal (the detail of the target you photographed). As you combine them, the signal (which is conserved across the pictures) builds in strength, while the noise tends to cancel itself out. The result is an image with more signal and relatively less noise giving more detail than you could ever see in a single photograph. To the left is a good example of the improvement in quality you might expect to see as you stack more photos or frames.

In addition, the bit depth of the image, which is the precision that an image can define a colour, also increases as you stack. For example, it you have a single 3-bit pixel (it can show 2³=8 values, i.e. from 0 to 7) a single image may measure the brightness of a star as 5, but the true value is actually 5.42. In this scenario, taking 10 photos, each giving the star a slightly different brightness value, may give you 5, 5, 6, 5, 7, 6, 4, 5, 5 and 6, the average of these being 5.4 – a more accurate value than the original, single shot, reading. The end result is a photo with lots of subtle detail that fades smoothly into the blackness of space.

So here are my final images of the Crescent and Dumbbell nebulae after I stacked over 40 frames each taking 3 minutes to capture (giving a total exposure of 2 hours each).

Screen Shot 2016-07-29 at 18.08.18

Was it worth being bitten to death by midges, setting my dog off barking at 4am, putting my wife in a bad mood for the whole next day…I think yes!

Post by: Daniel Elijah

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The Human Sensor: Making the Invisible Visible

July 22, 2016 by The Brain Bank North West

Breathe. Breathe deeply. Breathe in, breathe out. With each breath in, breathe in peace, tranquillity and calm. With each breath out, release tension, anxiety and pain. Let your mind be still, and your body relax, with an ever-present focus on your breath.

Such words and ideas may sound very familiar, and take you to a place of calm. Or they might sound completely foreign and a flight of fancy. The truth is, precious few of us in our daily lives ever consider our breathing outside of an escapist yoga class. But how many fewer of us, when we think about our breathing, take a moment to consider what might be in the air that we are breathing, and how that might be affecting us?

Air pollution is without doubt one of the biggest problems faced by the world’s cities. As estimated by the World Health Organisation, air pollution exposure causes 7 million premature deaths each year – one in eight of all global deaths. Whilst a significant number of these deaths occur in China (where there are estimated 4,000 premature deaths each day caused by air pollution) and India (where the non-smoking populace has a 30% lower lung capacity), Europe isn’t nearly as clean as it could be. A report from the EU’s European Environment Agency (EEA) says pollution is now the single largest environmental health risk in Europe, responsible for more than 430,000 premature deaths.

Closer to home, the picture remains grim. Manchester is the second most polluted city in the UK, and one of the most polluted cities in Europe. In Greater Manchester, the annual mortality estimate is over 1,000. But what actually are the pollutants that are causing all this damage?

One of the most significant is PM 2.5 , which is particulate matter condensed in air with a diameter smaller than 2.5μm (mainly sulphates, nitrates and carbon). These are nasty mixtures of combustion particles, metals and sulphates, and at less than 5% the diameter of a human hair, they can penetrate deep into the lungs. They have been linked to heart disease and lung cancer, and cause an estimated 29,000 premature deaths in the UK.

In addition, nitrogen compounds such as Nitrogen Dioxide (NO 2 ) form from the combustion process in vehicles. Long term exposure to NO 2 reduces lung capacity and lowers resistance to respiratory infection. The UK fails to meet the EU air quality standards for this pollutant, and exposure to NO 2 results in an estimated 23,500 premature deaths across the country.

According to the World Health Organisation, air pollution is the biggest public health problem faced by the developed world. But as we walk through busy streets, we never consider these effects. Apart from the odd stench of fumes from a bus or a lorry that we might notice, the fine particulates are undetectable to our senses and invisible to us. The cold statistics and hard science don’t relate to our daily experience. If we perhaps were more actively aware of how serious a problem this is, we might feel more inclined to drive less, or take more walks in the park, or simply avoid the busy streets. So how can we be more acutely aware of the science in our daily lives?

One way of connecting ourselves to certain issues and facts is through art. Music, dance and painting have all deeply emotionally resonated with us for millennia, in ways which science cannot. So scientific, socially conscious art could pave the way forward.

Screen Shot 2016-07-22 at 23.02.54 In collaboration with Manchester European City of Science, the non-profit organisation Invisible Dust have commissioned the artist Kasia Molga to create a show in the streets of Manchester that brings this issue out into the open. Called the ‘Human Sensor’, dancers will wear futuristic suits that light up in different colours depending on what they are breathing, making tangible the effects of poor air quality.

These live performances take place across the 23rd-29th July, with the launch at 7:30pm on no.70 Oxford Road (formerly the Cornerhouse). Invisible Dust are also hosting an information space there, open from 23–29 July, 1–5pm weekends and 1–9pm weekdays with free drop-in talks and workshops every day.

If you want to bring yourself into the present, become more aware of your surroundings and the world around you, then focus on your breathing. But remember there is more to the world around us than what we see.

Guest post by: Carl Thomas

Learn more about the project here:

invisible dust

Human Sensor

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Are we ready to live without immunisations?

July 17, 2016 by The Brain Bank North West

Screen Shot 2016-07-17 at 17.47.46 The immune system is like an army, poised and ready to attack: it actually comprises two separate systems, these being the innate and the adaptive immune systems – you could think of these as two separate groups of soldiers i.e. foot soldiers and intelligence officers. The innate immune system responds quickly to threats, it is always on guard but this system is non-specific, meaning that it does not recognise any specific threats and will respond to all threats in the same way – this system could be thought of as the bodies foot soldiers (recognising all types of enemy but always launching the same type of attack). The adaptive immune system is slower since it needs time to recognise the threat but, once this is done, this system can launch a more specific, targeted, attack. This system also has a memory, meaning that after successive encounters with the same threat it will adapt and the next time it encounters the same threat its attack will be faster and more efficient. It is during this type of attack that antibodies are produced. These antibodies stick around in the body and help bolster our immune system and speed up future attacks (it is this process which is augmented through immunisation/vaccination). We could think of this system as the body’s intelligence agency, gathering information on its enemy and launching a targeted attack.

When we receive a vaccine we are attempting to induce an immune response without harming the body. The body is infected by a harmless version of a virus or bacteria that triggers an immune response without making the recipient sick. This then creates an immunological memory so that the next time we are infected by the same pathogen the immune system will be quick to react and the threat will be neutralised before we show any symptoms.

Vaccines have been a major success, they have helped to eliminate most of the childhood diseases that historically caused millions of deaths and are very cost effective. Thanks to this, average life expectancy has increased from 35 years in 1750 to above 80 years today. According to World Health Organization measles vaccination resulted in a 79% drop in measles deaths between 2000 and 2014 worldwide, and according to UNICEF each year immunisation prevents around 2-3 million deaths a year from life-threatening diseases in children.

But some people still choose not immunise their children, stating a range of reasons – from religion to the belief that vaccines are neither effective nor safe. In 1998 the Lancet published a paper by Andrew Wakefield stating that the measles vaccine produced autism in 21 children. Later several peer-reviewed studies failed to show any association between the vaccine and autism and eventually the Lancet’s editors fully retracted Wakefield’s paper claiming deliberate falsification. But, despite a lack of solid evidence and the paper retraction, vaccination rates in the UK dropped to 80% in the years following, leading to an increase in cases of measles across the UK – causing not only deaths but also measles encephalitis. By 2008, measles had become endemic in the UK due to low-vaccinated communities.

Last year there was a case of diphtheria in Spain when a 6-year-old non-immunised boy became infected. Diphtheria is a highly contagious disease caused by a bacterium called Corynebacterium diphtheria. Thanks to immunisation campaigns in Spain the number of cases of diphtheria in the country dropped from 1,000 cases in 100,000 inhabitants in 1945 to 0.10 cases in 100,000 in 1965 – now in 2016 diphtheria is thought to have been eradicated in this area. Therefore when this young boy fell ill last year there were no treatments available in the country at the time. Sadly, despite heroic efforts to import a treatment, the child died. When his parents were asked why he had not been immunised they said they felt tricked and not properly informed by anti-vaccination groups; they thought they were doing the best thing for their child.

So what happens when people decide not to immunise their children? :

Assuming that a large proportion of a population are immunised it is possible that non-immunised individuals may be protected by a process known as herd immunity. Basically, the more people who are immunised, the fewer opportunities a disease has to spread – this confers protection to those who can’t be immunised (such as children with cancer receiving chemotherapy or radiotherapy, children treated with immunosuppressed drugs such as corticosteroids, people with weakened immune system or people allergic to any of the components of the vaccine). This means that these people really depend on those around them being immunised.

We can lose sight of the benefits of immunisation because we don’t have a memory of living in a world without vaccines. But, diseases that we thought were eradicated a long time ago will come back if we stop immunisation – meaning we could find ourselves confronting epidemics of diseases with the ability to kill hundreds of thousands of children and adults every year. Sadly some diseases will never be fully eradicated because they are found everywhere. For example, tetanus is a serious infection caused by Clostridium tetani bacteria which produces a toxin that affects the brain and nervous system. Clostridium tetani spores can be found most commonly in soil, dust and manure, but also exist virtually anywhere. So a child playing in a sand pit or with just some grass can get in easily infected through a cut or wound on his hands. Therefore, maintaining immunisation is particularly important in the fight against this type of disease.

Although vaccines do come with some side effects, like high temperature or soreness in the injected site, very serious health events post-immunization are rare and the benefits of immunisation clearly exceed the risks of an infection. Thus, the only way to prevent the infection is through immunisation.

Post by: Cristina Ferreras

References:

Rappuoli R et al. Vaccines for the twenty-first century society. Nat Rev Immunol. 2011 Nov 4;11(12):865-72. doi: 10.1038/nri3085. Erratum in: Nat Rev Immunol. 2012 Mar;12(3):225

UNICEF_immunization Facts and Figures April 2013 http://www.unicef.org/immunization/file/UNICEF_Key_facts_and_figures_on_Immunization_April_2013%281%29.pdf

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The functions of bioluminescence brought to light

July 10, 2016 by The Brain Bank North West

When picturing the dead of night or the deepest depths of the ocean, we may be inclined to think of pure, impenetrable darkness. Yet nature has quite a different image in mind – one where darkness is pierced by flashes of light, warming glows and pulses of colour. These vibrant light displays are the result of a phenomenon known as bioluminescence – the production and emission of light from a living organism, which occurs when a molecule called luciferin combines with oxygen in the presence of the enzyme, luciferase. Apart from being undeniably beautiful to watch, there is increasing evidence to suggest bioluminescence has a number of important functions for an organism.

Screen Shot 2016-07-10 at 11.41.10 Bioluminescence can occur in a broad range of organisms, from bacteria to fish (with the exception of higher vertebrates, e.g. reptiles and mammals), and is found across a variety of land and, more commonly, marine environments. In fact, around 60–80% of deep sea fish are thought to be bioluminescent. The pattern, frequency and wavelength (i.e. the colour) of light emitted can also differ by species and habitat. For instance, while violet or blue light is more common in deep water, bioluminescent organisms found on land tend to produce green or yellow light.

Bioluminescence lends itself to a number of functions – the first being for reproductive success. The most prominent examples of bioluminescence’s advantage in this area are in fireflies and glow-worms. In species of firefly where only the males are able to fly, the females attract their mate by emitting a constant glow which can be spotted by the males as they fly overhead. In other species, the male fireflies are also bioluminescent and produce a flashing light in response to the female’s glow. This results in a kind of “courtship conversation”. It has been suggested that the female’s preference may be determined by the frequency of male flashes, with higher flashing rates being more desirable. There are also a variety of fish in the deep ocean which appear to use bioluminescence to facilitate reproduction. Black dragonfish, for instance, are unusual in the fact that they emit a red infrared light, rather than the blue light common to deep-sea organisms. In doing so, however, dragonfish are able to use this light to seek out a mate in the darkness without alerting prey to their presence.

Screen Shot 2016-07-10 at 11.41.17 In contrast to hiding from prey, as with the dragonfish, bioluminescence can also be used to attract prey. Deep in the Te Ana-au caves of New Zealand, fungus gnat larvae construct luminescent “fish lines” to lure other insects. These insects then become trapped on the sticky lines and become a tasty meal for the lurking larvae. Back in the ocean once more, there is evidence that a type of jellyfish, known as the “flowerhat” jellyfish, also uses bioluminescence to attract small fish (e.g. young rockfishes) on which it preys. These jellyfish have fluorescent patches on the tips of their tentacles. In experiments studying how tip visibility influences predation, it was found that significantly more rockfish were attracted to the jellyfish with visible fluorescence than when the fluorescence was indiscernible, highlighting the importance of this attribute to this organism in acquiring food.

Alternatively, bioluminescence may also be useful to protect an organism from predation. This can work in a variety of ways, from providing camouflage to acting as a warning signal to predators against the dangers of attacking. A good example of the latter of these functions can be seen in glow-worm larvae. Unlike adult glow-worms whose fluorescence aids courtship, glow-worm larvae emit light to warn predatory toads of their unpalatability. This has been demonstrated by researchers in Belgium who found that wild nocturnal toads were more reluctant to attack if dummies resembling the larvae were bioluminescent. In addition, bioluminescence can work to protect against predation by acting as a diversion technique. Some species of squid, for example, are able to release a luminescent secretion when under threat, confusing the predator so they can escape.

For now, the role of bioluminescence seems to be clearer in animals than in those organisms outside the animal kingdom, such as fungi or bacteria. There is, however, a recent study which has suggested a potential role for bioluminescence as a method of spreading spores for a certain variety of mushroom found in Brazilian coconut forests. The investigators in charge of this study were able to attract nocturnal insects using an artificial light which replicated the mushroom’s green bioluminescence. This did not happen when the light was switched off, suggesting light may be used to help this type of mushroom entice insects which can then disperse its spores.

Bioluminescence can provide its creator with a light in the darkness. It can help an organism to seek out, attract and successfully court a mate; lure unsuspecting prey to their doom, and warn off or divert the attention of predators when under attack. Yet while there are a many instances where the function of bioluminescence is fairly clear, as discussed here, scientists remain very much “in the dark” in other cases. This is particularly true for those organisms, such as fungi and bacteria, which do not belong to the animal kingdom. Nevertheless, with continued research and new discoveries forever being made, it is only a matter of time before these elusive functions are brought to light.

Post by: Megan Freeman

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Are you my type? The fascinating world of blood types

July 4, 2016 by The Brain Bank North West

With our 30th birthdays on the horizon my best friend and I decided to make a bucket list. As the months ticked by one thing on my list stood out – blood donation. I must admit I feel slightly ashamed that, peering over the horizon of the big 30, I’m yet to give blood, especially since both my mum and maternal grandmother donated so regularly in their youth that they were given awards. My grandmother always told me she felt compelled to donate since she had a relatively rare blood type*. She also told me that the reason my mother was an only child was because of an incompatibility between my mother’s blood, which was positive for a blood factor, and her own, which was negative (https://en.wikipedia.org/wiki/Rh_disease). This got me thinking – how many blood types are there, and why do they exist? How is it that the blood flowing through my veins and yours can be made of the same basic elements and yet be so different?

All human blood consists of the same fundamental components – red blood cells, white blood cells, plasma and platelets. Of these, it is the red blood cells that give the blood it’s identity or ‘type’. The surface of red blood cells is covered with molecules, and the presence or absence of a particular molecule determines which blood group you belong to. The principal blood grouping system used for humans is the ABO system which categorizes people into one of four groups – A, B, AB, or O on the basis of the presence or absence of a particular antigen. An antigen is a molecule capable of producing an immune response only when it does not originate from within your own body. For example, a person with type B blood who has the B antigen on their red cells could not receive blood from a person of blood type A, since the A antigens on this donor’s blood would be foreign to the type-B recipient’s body and would therefore cause an immune response. People with blood type B have the B antigen on their red cells whilst type A people have the A antigen. If you belong to AB, your red cells have both A and B antigen types and if you are group O you have neither A nor B. This basic grouping can be expanded to 8 groups when another important factor ‘Rh’ is considered. The Rh antigen can either be present (+) or absent (-), so if like my grandmother you have A- blood it means that your red cells have A antigens and are negative for the Rh factor.

At first glance categorizing blood into different types may seem like an academic exercise or a scientific curiosity but it has serious real world consequences. In the 1800s many doctors noted the seemingly unnecessary loss of life from blood loss; however few were brave enough to attempt transfusions. This reluctance stemmed from earlier attempts at transfusion in the 1600s in which animal blood was transfused into human patients. Most of these attempts ended in disaster and by the late 1600s animal blood transfusions were not only banned in both Britain and France but also condemned by the Vatican. However, after watching another female patient die from haemorrhaging during childbirth, the British obstetrician James Blundell resolved to find a solution. He thought back to the earlier transfusion attempts and correctly guessed that humans should only receive human blood. Unfortunately, what he didn’t realise was that any given human can only receive blood from certain other compatible humans. Blundell tried but with mixed success, and by the late 19th century blood transfusion was still regarded as a risky and dubious procedure that was largely shunned by the medical establishment.

Finally in 1900, the Austrian doctor Karl Landsteiner made a breakthrough discovery. For years, it had been noted that if you mixed patients’ blood together in test tubes, it sometimes formed clumps. However, since the blood was usually taken from people who were already ill, doctors simply assumed that clumping was caused by the patient’s illness and this curiosity was ignored. Landsteiner was the first to wonder what happened if the blood of healthy individuals was mixed together. Immediately he noticed that some mixtures of healthy blood clumped too. He set out to investigate this clumping pattern with a simple experiment. He took blood samples from the members of his lab (including himself) and separated each sample into red blood cells and plasma. Systematically, he combined the plasma of one person with the red cells of another and noted if it clumped. By working through each combination he sorted the individuals into three groups which he arbitrarily named A, B, and C (later renamed O). He noted that if two individuals belonged to the same group, mixing plasma from one with red blood cells of the other didn’t lead to clumping- the blood remained healthy and liquid. However, if blood from an individual in group A was mixed with a sample from an individual in group B (or vice versa) the blood would clump together. Group O individuals behaved differently. Landsteiner found that both A and B blood cells clumped when added to O plasma, however he could add A or B plasma to O red blood cells without clumping. We now know that this is because red blood cells express antigenic molecules on their surface. If an individual is given blood of the ‘wrong’ type (i.e. one that expresses a different antigen to the host’s blood) the person’s immune system notices that the transfused blood is foreign and attacks it, causing potentially fatal blood clots. Our knowledge of different blood types means that we can now make safe blood transfusions from one human to another thereby saving countless lives. In recognition of this fundamental discovery, Karl Landsteiner was awarded the Nobel Prize in Physiology or Medicine for his research in 1930.

Since Landsteiner’s work, scientists have developed ever more powerful tools for studying blood types. However, despite increasingly detailed knowledge of the genes and molecules expressed by different blood groups, it’s still unclear why different types exist at all. In an effort to understand the origins of blood types, researchers have turned to genetic analysis. The ABO gene is the gene responsible for producing the antigens expressed on the surface of our red blood cells. By comparing the human gene to other primates, researchers have found that blood groups are extremely old – both humans and gibbons have variants of A and B blood types and those variants come from a common ancestor around 20 million years ago.

The endurance of blood groups though millions of years of evolution has led many researchers to think that there could be an adaptive advantage to having different types. The most popular hypothesis for the existence of blood types is that they developed during our ancestors’ battles with disease. For example, if a pathogen exploited common antigens as a way of infecting its host, then individuals with rarer blood types may have had a survival advantage. In support of this, several studies have linked different disease vulnerabilities to different blood groups. For example, people with type O blood are more protected against severe types of malaria than people type A blood, and type O blood is more common in Africa and other parts of the world that have a high prevalence of malaria. This is suggestive of malaria being the selective force behind the development of type O blood.

As I sign up for my first blood donation appointment I think back to everything I’ve learnt about blood types. I’m eager to find out what my blood type is and what that might mean about the history of my ancestors, and the disease challenges they’ve faced. Most of all though I’m excited to continue my family’s tradition and contribute to one of the humankind’s greatest medical advancements.

Post by: Michaela Loft

*A- which is only present in ~7% of caucasians.