September 2016 – The Brain Bank North West

Cakealicious science: The science of baking

September 26, 2016 by The Brain Bank North West

Food glorious food! Cakes cakes and more cakes! These sweet creations have had people drooling for centuries. There are many variations from rich chocolate to fruit and nut, covered in buttercream or marzipan, stuffed with jam or cream, the choices are almost endless. They’re perfect for big celebrations or just a chilled out half hour with a cup of coffee. But how on earth do they actually work? How can butter, sugar, flour, eggs and baking powder combine to make a delicate mouth-watering sponge?

Magic?

screen-shot-2016-09-26-at-08-15-46 Well science magic anyway. Each key ingredient has its own special role, without which the cake would collapse. The major ingredients need to be roughly of equal weights. First off the sugar and fat are mixed together. During the mixing process air gets caught on the rough surface of the sugar granules and is sealed in by a film of buttery fat, this forms a light fluffy mixture akin to whipped cream. We use caster sugar in this process rather than granulated sugar because it is finer than granulated sugar and therefore has a greater surface area on which to trap air.

screen-shot-2016-09-26-at-08-16-25 But sugar does more than just trap air within the cake batter. It softens the flour proteins tenderising the mixture, it also lowers the mix’s caramelisation point, allowing the crust to develop a crisp golden consistency at relatively low temperatures. Finally, sugar also helps keep the cake moist and edible for many days. Most of the moisture in a cake comes from the eggs, which provide the mix with the majority of its liquid. When everything is mixed together the eggs produce a foam which surrounds the air bubbles in the mixture protecting them from the heating process and which is also stiffened by starch in the flour. Proteins in the flour join together creating a network of coiled proteins that we know as gluten. Gluten is key to holding the cake together, it expands during baking and then, when cooling, coagulates and is able to support the cake’s weight.

For the bakers out there you may have noticed that we have missed out the baking powder, this may come across as some voodoo magic but it is basically just dried acid and an alkali. Adding water and heat to this mix allows them to react producing CO2.

Now it’s not just getting the right measurement of ingredients, but it’s also essential to get the temperature of the oven precisely right. Too low and the expanding gas cells coagulate producing a coarse heavy texture leading to the cake sinking, too hot and the outside starts setting before the inside even finishes baking, leading to a volcano-looking cake.

So when you next grab a cupcake just take a little time to appreciate the exact science that went into baking that mouth-watering little treat. So many things that could go wrong it’s a miracle we ever found out how to make these soft icing covered delights.

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Post by: Jennifer Rasal

Sources:

https://www.theguardian.com/science/blog/2010/jun/09/science-cake-baking-andy-connelly

https://en.wikipedia.org/wiki/Cake

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Woody Plants and pharmaceutics

September 19, 2016 by The Brain Bank North West

Take a moment to think about your health over the last year. How often have you taken a painkiller to manage that headache or fever? These powerful tools have the ability to save you from a day of pain, allowing the survival of that long shift at work or half-marathon which has slowly crept up on you. How many relatives or friends have had their health improved through life saving medications such as chemotherapy or anti-depressants. There are a large variety of medications widely used today that have transformed our lives and we would struggle in a world without them. Many are aware that it is advances in medical research which have enabled the development and availability of these. However, it is often forgotten that when developing such drugs scientists will usually take their inspiration from similar compounds found in nature. But where? This article gives much deserved recognition to nature’s own pharmacologists. After all, these magicians are our true heroes.

So, what natural marvels are responsible for these compounds? – mainly plants, animals and fungi. This article will focus primarily on woody plants and their ability to produce useful chemicals. The extraction of compounds from plants goes back years. From tribes making herbal remedies to the scientific extraction of the chemicals we use today. Below are a few examples of how woody plants have completely transformed our lives:

Aspirin:

screen-shot-2016-09-19-at-20-04-45 Aspirin is a silicate sold as an over the counter medication. Its main purpose is to reduce pain and inflammation. The active ingredient in this common drug originally comes from willow tree bark and has actually been used for about 6000 years. So, how does this drug work? Willow bark contains a substance called salicin which the body transforms into salicylic acid. This acid reduces the production of certain prostaglandins in our nerves. Prostaglandins are produced in response to tissue damage or infection, their role being to facilitate the healing process. However, alongside their healing properties they also cause pain, therefore reducing their production can minimise the pain associated with the healing process. It can subsequently be deduced that willow trees do much more for us than just creating a gorgeous aesthetic landscape!

Irinotecan:

screen-shot-2016-09-19-at-20-05-23 Irinotecan is a chemotherapy medication primarily used to treat colon and rectal cancer. The active ingredients within this medication include camptothecin, pentacyclic quinolines and 10-hydroxycamptothecin, which are derived from Camptotheca Trees, Camptotheca acuminata. The mechanisms by which these compounds interact with the human body are complex. They inhibit DNA topoisomerase I which is important for the replication of cancer cells. It would therefore make sense that without this substance, cancer cannot thrive. This is because type 1 topoisomerases are catalysts for the transient breakage of DNA and for the re-joining of the strands following this during cell replication. Without this catalyst, replication would occur at a very slow rate. Cancer is a devastating disease and advances such as this are hugely important.

Digoxin:

Top: Normal heart activity. Bottom: Heart fibrillation

Digoxin is well established in the treatment of heart arrhythmias including atrial fibrillation. It is extracted from the leaves of the common foxglove plant, Digitalis purpura. It works by slowing down the heart alongside improving ventricle filling which increases the blood supply available for each pump. The heart is one of the most important organs in the body, subsequently reflecting the importance of this medication and its lifesaving qualities.

These are just three examples of how woody plants have transformed our lives. However, there are still many unidentified species that have not yet been discovered in our ecosystems which have the potential to contain life-saving chemicals. In addition, there is the potential for the availability of medication that has fewer side effects to those currently in use. Unfortunately, many biomes are currently being destroyed at such a rate new species, and perhaps medically active chemicals, are being removed before any possible benefits can be uncovered. Therefore, the increased rates of deforestation may be destroying more than just habitats, they may be taking with them a wealth of potentially undiscovered medicines. This is just one more example of why conservation work is so important and I urge that it is taken seriously. Effective conservation is clearly vital to improve the lives of our future generations. It can be concluded that plants have played a huge role in our lives over many generations and continue to help us on a daily basis thus reflecting the importance of conserving them.

Take home message: Next time you take that aspirin in a moment of despair, take a moment to really appreciate the unsung heroes of pharmacy – woody plants. It is a shame that whilst many plants save us, we thank them by cutting them down, destroying biomes and causing extinction.

Post by: Alice Brown

References:

http://medicinalplants101.blogspot.co.uk/2014/01/camptotheca-aka-cancer-tree.html

http://sitn.hms.harvard.edu/flash/2011/where-does-medicine-come-from/

http://www.arthritisresearchuk.org/arthritis-information/complementary-and-alternative-medicines/cam-report/complementary-medicines-for-rheumatoid-arthritis/willow-bark.aspx

http://www.biologicaldiversity.org/publications/papers/Medicinal_Plants_042008_lores.pdf

http://www.ebi.ac.uk/interpro/entry/IPR018521)

http://www.kew.org/science-conservation/plants-fungi/digitalis-purpurea-common-foxglove

http://www.sciencedirect.com/science/article/pii/S1319610310000578

https://www.bhf.org.uk/heart-matters-magazine/medical/drug-cabinet/digoxin

https://www.drugs.com/aspirin.html

https://www.google.co.uk/search?q=Irinotecan&biw=1366&bih=667&source=lnms&tbm=isch&sa=X&ved=0ahUKEwiygLePlu7NAhXJB8AKHRwJBloQ_AUIBigB#imgrc=kiktTvOYld7YIM%3A

https://www.google.co.uk/search?q=type+1+topoisomerase&biw=1366&bih=667&source=lnms&tbm=isch&sa=X&ved=0ahUKEwishr_Uke7NAhULAsAKHZxHAeIQ_AUICCgB#tbs=sur:fc&tbm=isch&q=arrhythmias+&imgrc=rri9FbPzjvwvoM%3A

https://www.google.co.uk/search?q=willow+tree&biw=1366&bih=667&source=lnms&tbm=isch&sa=X&ved=0ahUKEwjxs7bnje7NAhXoC8AKHQhNC2YQ_AUIBigB#q=willow+tree&tbm=isch&tbs=sur:fc&imgrc=nDpmo_llPSg_1M%3A

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Are we finished editing CRISPR?

September 11, 2016 by The Brain Bank North West

The academic world has been abuzz in the last few years with talk of a new gene editing technology known as CRISPR. We hear about it on the news and are told that it could one day be a game-changer for modern medicine in terms of genome editing. But, like this article, all new techniques require proofreading and adaptation. So what I’m really wondering is: are we finished editing CRISPR?

CRISPR stands for ‘clustered regularly interspace palindromic repeats’, a mouthful even in the scientific community! CRISPR is a constituent of prokaryotic DNA and is used by these cells as a simple immune system, protecting them against viral attacks. We can imagine prokaryotic DNA as a piece of string (below: labeled as bacterial DNA), with repeated segments (circles) broken up by spacers (rectangles). Bacteria are able to detect invading viral DNA and add short sequences from the viral DNA in between the repeated sequences of their own DNA, creating a catalogue of past infections (a bit like our own immune system). If a virus attacks the same cell again these spacer regions are recognised by a special group of proteins called Cas proteins. Cas proteins are nucleases which use the CRISPR-incorporated viral DNA segments to chop up the infecting viral DNA and inactivate it.

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Scientists have harnessed the power of the CRISPR/Cas9 system by replacing viral DNA spacers with synthetic guide RNA’s that match a specific DNA sequence – this can be anything the scientist wants to modify. Researchers can then direct the Cas9 protein to their selected gene, causing a break in the DNA and the deletion of that region of the gene, ultimately allowing them to control expression of selected genes.

In theory CRISPR has the power to edit and even remove harmful genes associated with both acquired and hereditary diseases. In fact, just this year Anderson and colleagues at MIT demonstrated its potential in mice, correcting a harmful metabolic mutation. So why are we not using CRISPR in the clinics already?

While most people have no issue with treating acquired conditions, such as cancer, in previously healthy people, concerns arise when we talk about germline editing: i.e. editing human embryos prior to birth. From a medical perspective embryo editing could enable children with life threatening and debilitating conditions to lead a ‘normal life’. However, some parents believe that editing their child’s genome will change the child’s identity. Researchers also argue that, not only will germline editing reduce genetic diversity but we also don’t know enough about the genome and its regulation to confidently make such drastic and heritable changes. On a personal note, my main concern is where would germline editing stop? Where do we draw the line at disease state? For example obesity, my own area of research, and its predisposition is now considered as a disease. The more conditions we begin label as ‘diseases’ the easier it could be to edit for desired traits.

All these issues exist before we even begin to think about the safety aspects of this new technique. How do we deliver this system effectively into the human body? And, once there, how efficient and specific will it be. For example off target effects have ranged between 0.1-60%, levels still too risky for the clinics.

While acknowledging that CRISPR does have great potential in the future, much editing and rewriting may still be required before we can click submit.

Post by: Stephanie Macdonald

Sources:

http://www.nature.com/news/crispr-1.17547

http://www.nature.com/articles/nbt.2884.epdf?referrer_access_token=vn4y2fRlT6MSfnjiTkEah9RgN0jAjWel9jnR3ZoTv0NYT9zJj6mpbqWqBhkZTqLWByT9ZihiHupT0fSw150iFynOlHiUTmOgoLqeCBiezScmQzKXSWZlhANyZY8taAUjw7mxZP3DyqCYVeWMBSDBoB_ExZ0FQkLTfyBfhnOubzmO0jxfwklUENzc3pAW-hXzt-7A-uc2YpLGwekIaMKzouz-lsbrPIE9Dozc5RIYLf8%3D&tracking_referrer=www.nature.com

Figure adapted from:

https://en.wikipedia.org/wiki/CRISPR

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How to perfect your astro-photos.

September 5, 2016 by The Brain Bank North West

In my last post I discussed why astronomers take multiple identical photographs of the same astronomical object in order to reduce the effects of random noise. I discussed how this noise arises and gave examples of the improvements gained by stacking multiple photos together. Of course, reducing random noise within your image is an important first step but, if you really want to obtain the perfect astro image, there is still more to consider. Both your camera and telescope can introduce a number of inconsistencies in your images, these occur to the same extent in every photograph you take, meaning they cannot be cancelled out like random noise can. Here I will discuss what these inconsistencies are and the ways astrophotographers remove them.

So…what are these inconsistencies? Well they come in three types and each must be dealt with separately:

The first of these is a thermal signal which is introduced by the camera. This tends to look like an orange or purple glow around the edge of an image. It develops when heat from the camera excites electrons within the sensor. As we take a photo, these heat-excited electrons behave as though they have been excited by light and produce false sensor readings. This effect gets stronger with increasing exposure time and temperature. The best way to remove this is to take an equal length exposure at the same temperature as your original astro image but with no light entering the telescope/camera (perhaps with the lens cap on). The resulting picture will contain only the erroneous thermal glow. This ‘dark’ frame can then be subtracted from the original image.

fig_1 — Figure 1. The original exposure (showing the constellation Orion at the bottom) shows a strong thermal signal in the top left. By taking a dark frame of equal exposure, we can subtract out the thermal signal, giving a better result.

The next inconsistency is known as bias. This constitutes the camera sensor’s propensity to report positive values even when it has not been exposed to light. This means that the lowest pixel value in your picture will not be zero. To correct this, it’s necessary to shoot a frame using the shortest exposure and the lowest ISO (sensitivity) possible with your kit then subtract it from the original frame. For most modern DSLR cameras, this subtraction has a very small effect but it does increase the contrast for the faint details in the picture – which is particularly important when shooting in low light.

Finally, and arguably the most important image inconsistency of all – uneven field illumination. This problem occurs when the optics within a telescope do not evenly project an image across the camera’s sensor. Most telescopes (and camera lenses) suffer from this problem. A common cause of uneven illumination is dirt and dust on the lens or sensor, which can reduce the light transmitted to parts of the sensor.

This is the objective lens from my telescope before and after cleaning. Although small specs of dust do not seriously affect the overall quality of the image, they can contribute to uneven brightness in the image.

The final cause of uneven illumination is vignetting, this is a dimming of the image around its edges. Vignetting is normally caused by the telescope’s internal components such as the focus tube and baffles (baffles stop non-focused light entering the camera). These parts of the telescope can restrict the fringes of the converging light from entering the camera. So how do we combat this…keep cleaning the lens? Rebuild the internal parts of the telescope?…no. The answer is simple; take a ‘flat’ calibration frame. All you need to do is take an image of a evenly illuminated object (such as a cloudy sky, white paper, or blank monitor screen). Since you know the original scene is uniformly bright, any unevenness in the brightness of this image must be due to issues with the telescope. You then divide the brightness of the pixels in the original image by the pixels in the flat frame and magically, the unevenness is gone.

For your enjoyment, here’s some examples of flat frames taken from across the Internet, the middle image is from my scope. There are some diabolical flats here; I wonder if it’s even possible to conduct useful astronomy with such severe obstructions in a telescope!

Some examples of flat field frames taken by different telescopes. All these frames show were light is being blocked from reaching the camera sensor. My telescope’s flat frame is the middle picture; it looks good in comparison.

By applying the flat frame correction, the background of the image becomes more even, and dark patches due to dust disappear! No need to clean your scope! (Image taken from http://interstellarstargazer.com).

For many people starting to turn their cameras and scopes to the heavens, all of this does sound rather arduous but there is software out there that will automatically combine your star images with the three calibration images and spit out what you want (see Deep Sky Stacker). I was amazed that for reasonably little effort and no extra money, I could improve the quality of my images significantly.

Post by: Daniel Elijah