Why Do We Hiccup?

Hiccups are an interesting phenomenon which everybody experiences at some point in their lives and there are many theories around why they happen. The first thing to understand is what they are. There are two different muscles involved in breathing, the diaphragm – a muscle below the lungs – and the intercostal muscles – muscles attaching the lungs to the ribs. Hiccups happen when these muscles become out of sync, causing the diaphragm to contact violently.

So we know what they are, but the question is why do they happen? And what is their purpose? The short answer is, we don’t know. Though there are many interesting theories.

IT has been noticed that although there is no obvious trigger, they are more likely to happen when a person has eaten or drunk something quickly, particularly fizzy drinks. Though hiccups obviously don’t always occur every time after you drink fizzy drinks. Other noted triggers are drinking alcohol and smoking, but these are rare occurrences when compared with the number of cigarettes an individual smokes a day or how often an individual will drink alcohol.

Clearly there is something else going on here, as another fact is that hiccupping is more common in babies, than adults. Did you know, that hiccupping has also been witness happening in foetus’ in the womb, suggesting that it could have an evolutionary mechanism.

From an evolutionary standpoint, in 1997 it was suggested that hiccupping had developed to prepare the respiratory muscles of the foetus for breathing after birth and also for clearing the lungs when fluid moved into them and shouldn’t be there. Which also could suggest that it helps suckling infants by preventing milk from accidently getting in to their lungs (see next paragraph). This is not, on the surface, a satisfactory explanation as a hiccup is more likely to cause a baby to ‘suck’ things/ fluids into the lungs rather than expel them.

One theory is that hiccups help with suckling in infants, preventing milk from getting into the lungs. This is a theory that comes from a theory about why hiccups may have existed in the evolution of humans in the first place. A mechanism very similar to hiccups is seen in many amphibians, forcing water away from the lungs and over the gills. This is a strong possible theory, particularly given that hiccups are seen in other mammals besides humans, but begs the question of why has it prevailed so long in evolution of fully terrestrial animals? An interesting theory on this is due to breast feeding, helping babies to learn to suckle without getting milk into their lungs. Though the process of hiccupping and suckling have similar mechanisms. This would also help explain why infants hiccup more than adults, but there are many muscles involved in suckling which are not involved with hiccupping, which leads to this being as highly flawed theory.

With all this in mind, many people have different ideas of ‘cures’ for hiccups. The simple truth is that none of these have been proven to work, but they are interesting non-the less. There are some common cures that are well known and some less common ones. The common ones appear to be: holding your breath, being scared, and drinking water upside down. Some others that I am aware of are putting salt under your tongue, swallowing whilst holding your breath (harder than it sounds), gargling with ice water, putting a cold key down your back (what?!), reflexology and breathing into a paper bag. If you Google ‘hiccup cures’ the list is never ending!

Breathing into a paper bag is the only one of these cures that appears to have some sort of biological basis, as it could be argued that it is linked to the evolutionary theory linking us to amphibians. The amount amphibians breath using their gills decreases with an increased amount of carbon dioxide (CO2) and because of this it is thought that breathing in more CO2 will reduce hiccups. Breathing in and out of a paper bag causes you to breath in air you have just breathed in, which have a much higher concentration of CO2 than the air we normally breath in.

Another suggested theory is that the first hiccup is the only one that is real and the rest area phycological. This is a weird suggestion, let me explain. The suggested reason for this is due to the first hiccup being a response to the body reacting to thinking it is drowning (which does seem to makes sense that this would happen if we eat or drink too fast), and the rest of the hiccups are the body continuing to respond to the initial stimulus. This can be some what supported by the fact that no cure has been shown to work, but people swear that they do. It’s a placebo effect, if you believe something will cure you then it will, particularly of hiccups are all in your head to begin with. The issue with this is that there is no scientific basis for it and this still doesn’t explain why they would happen in the first place!

The take home message from all this is that we simply don’t know what causes hiccups, but as they are not life threatening, then it seems okay that this is the case for now.

References

Iflscience is a very good reference for a lot of things:

http://www.iflscience.com/health-and-medicine/why-do-we-hiccup/

This website has a lot of information, though is very technical:

http://gut.bmj.com/content/41/5/712.full

Some interesting theories on here as well, though much less information:

http://wonderopolis.org/wonder/how-do-you-get-rid-of-hiccups

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A New Cancer Detection Method

Cancer is one of the main killers of humans worldwide and the number of cases is increasing every year due to increasing populations and life expectancy. Just this year scientists in Istanbul have finished designing a highly sensitive sensor that can detect early stage cancer cells. Though still in the early stages of development, it has great potential to save many lives as current cancer detection methods are very expensive which can result in doctors avoiding performing these tests due to their expense and they often require specialists to perform them. One of the problems with the current cost, it that doctors may avoid having these tests performed because of their expense. This method could be cheaper, and may be performed and interpreted by non-specialist staff and since it can detect early stage cancer cells could save lives, as The obvious importance to this is the sooner cancer can be detected, the sooner it can be treated and less people will die from cancer because of it.

One of the problems with detecting cancerous cells is that they’re just normal body cells that simply won’t stop multiplying. Mutations in the DNA cause the cells to divide out of control without stopping like they should do normally. The picture below shows confocal images of cancer cells as they grow and develop over several hours. A is 24 hours, B is 48 hours and C is 72 hours. It is clear to see how quickly they can grow in just a short space of time.

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Figure 1 – taken from (Dervisevic et al 2017)

This makes cancerous cells difficult to detect under a microscope as they look more or less like normal tissue cells until they reach very late stages. The only way to detect the changes to these cells is on the molecular level, which is why the technology to do this is so expensive.

One change that does occur is to the antigens on the surface of cancer cells, which are structures that basically allow specific receptors on other cells to recognise the cells around them. Normally this would be enough for the body’s immune system to spring into action and identify and destroy any cells with unrecognised antigens. The cancerous cells have the ability to counteract this by over producing sialic acid by around 1000x more than normal healthy cells, which protects them from the immune response.

The new method developed by Dervisevic and the rest of team which is described in this paper looks into electrochemical methods as an early detection technique to identify these antigens on cancerous cells. These cancer detection methods are not new (REFERNCE), but the problem with them is that they are not specific enough to be reliable.

So, what are electrochemical methods?  Electrochemical means something that is able to generate electrical energy from a chemical reaction. Basically the way this works is that the acids used react with antigens and cause chemical reactions which then produce an electric current that can then be detected and measured.

To run their experiments Dervisevic et al used both cancerous cells and healthy cells, using bone marrow in each case. They chose boronic acid for the reactions, as it has previously been used successfully to identify tumour cells. The team also used a variety of different tools to detect the electrochemical response.

The experiments found that this method had a lower detection limit of 10 cells mL−1, suggesting that this method will be useful in detecting early stage cancer, because it can identify such a small amount of cancer cells. The method was also very accurately able to differentiate the cancerous cells from the healthy cells, which proved its use as a diagnostic tool.

I found the paper itself is quite arduous to read because it is so jargon heavy. There were many technical terms within the paper that not all seemed to be explained well. However, I have only given an overview of what the paper is looking at, the actual details of the paper go into much more complex detail.

The results are still in early stages and a lot more testing needs to be done before this is available as a proper diagnostic tool. For example, despite having many cell lines generated, all the cells used came from a very small number of individuals. It would be important to have a wide variety of individuals; to ensure this method would work for all types of people. There can also be difficulties in extracting bone marrow, so it’s not yet clear if the procedure as a whole could be used by non-specialists as it currently is.

However should further tests also be successful, down the line the findings of this paper really could save a lot of lives!

http://www.sciencedirect.com/science/article/pii/S0956566316311198#gr2

GM Humans, Closer Than You May Think

Since the successful cloning of Dolly the Sheep in 1996 there have been many issues (both morally and scientifically) with genetically modifying plants and animals. The controversy increases further as scientists look into editing human genetics. In February of last year (2016) Britain became the first country that has been allowed to genetically alter developing human embryos.

An article in The Guardian explained the basis of how this works quite well. Here it is should you wish to read it yourselves:

https://www.theguardian.com/science/2016/feb/01/human-embryo-genetic-modify-regulator-green-light-research

This research could be incredibly important as there is still a lot we don’t know about our own development and what we can learn from other organisms about this is limited. With genetic techniques advancing so quickly there are so many potential possibilities of further advancements we could achieve through research with human embryos. This includes the possibility of irradiating diseases and also potentially discovering why so many miscarriage happen.

There are many genetic techniques that can be used on embryos, it really depends what the goal is. Many methods have become outdated due to one big discovery – CRISPR. This is a new and fantastic method of very specifically altering the embryonic DNA. It was discovered in bacteria as part of their defence mechanisms to protect them from viruses. CRISPR stands for “clustered regularly interspaced short palindromic repeats,” which is one hell of a mouthful and does sound very technical, but don’t worry, it will make more sense shortly. In bacteria it works by the bacteria cutting the viral DNA into small pieces and inserting these small fragments into their own DNA. That way if the virus attacks them again, they will be able to recognise it. We can mimic this by recreating the enzymes that are needed and can use these to cut desired sequences and put them into chosen DNA sequences. It is a bit of a complex process; this video is funny and explains it quite well:

https://www.youtube.com/watch?v=k99bMtg4zRk

CRISPR is incredibly complex and interesting and I would love to go into more detail here, but am unable to do so without writing a long essay! If you would like more information on the subject then there are more links at the end.

There are obviously many concerns about embryonic research and I am going to look at a few of them. But first I must make a few things clear about the law and biology behind all this. The embryos are not allowed to develop past 14 days, and are not allowed to be implanted as part of IVF treatment. After these 14 days they have to be destroyed. No baby will be born that a scientist has genetically modified, at least not in the immediate future. Also, unlike other animals, human embryos have to be voluntarily donated to be used, they can’t just be taken from IVF clinics or anything like that!

Stem cell research is already a thing, how is this any different?

Stem cell research works only with very early zygotes. A zygote is an egg that has just been fertilised, and only becomes an embryo at 12 days. Stem cells are cells that can become any tissue although they only retain this ability for a very short period of time. Just one day after fertilisation the cells have already begun to specialise towards becoming specific parts of the body and are no longer truly stem cells. What is the significance of 14 days? After this point the egg begins to develop human features, the cells begin to specialise and the human form starts to develop.

Human embryo testing is an emotive subject for many people and many concerns have been raised and amplified due to Britain being allowed to test on them.  However, the possibilities for potential breakthroughs in genetic disease prevention is phenomenal. Diseases such as sickle cell anaemia, cystic fibrosis, Huntington’s, Duchenne muscular dystrophy, Epidermolysis Bullosa, haemophilia are a few of the many debilitating and life limiting diseases that could potentially be eradicated. You can see from this list just how many diseases could be helped with this research, and that’s not even scratching the surface. There have been mixed responses and while many people believe that it is a good and positive thing to help treat disease, they believe we shouldn’t go any further with it.  In this post, I have tried to address some of the key issues for you.

What if this leads to the production of designer babies?

This is a genuine concern, expressed by many and although it doesn’t affect us now and won’t do in the immediate future, the potential for a Gattaca scenario to happen is a very real possibility.  For anyone who doesn’t know what Gattaca is; it’s a science fiction film set in a future where most people are no longer born naturally, they are born by genetic engineering of selected genes. This has led to a society that decides what you can and cannot do or have, including employment, based solely on your genetics. The main character of the film is a man who was born naturally and so doesn’t have pre-programmed perfect genetics and so struggles in this futuristic society. This film was made in 1997 and clearly highlights the genuine fear of possible prejudice based on the science of ‘designer babies.’ I highly recommend watching the film, so here’s the IMBD link for you to have a look:

http://www.imdb.com/title/tt0119177/

One of the main benefits of allowing genetic altering in human embryos is the potential to wipe out genetic diseases, as I mentioned above. Once the technology reaches a point where it is able to do this, then restrictions can be placed to only allow for genome editing preventing babies being born with life affecting diseases. But could this in itself become a slippery slope towards over stepping the boundaries of what it is justifiable to edit?

Herein lays the dilemma of arguments for and against genetic engineering. On the one hand the technology can save the suffering of so many babies but on the other it may lead to a Gattaca situation in the future!  It is possible to argue that, for example, people who are colour blind cannot do certain jobs because they see a reduced number of colours. Is it possible to argue that their lives are negatively affected by this and this should be something we should correct in new babies? And if we can ask that about one thing, why not another? Do we correct for short sightedness when this could easily be corrected with glasses? Where does it end?

Who decides what is acceptable genetic modification?

This is a tricky thing to answer and I honestly don’t know the answer. This is the kind of question that is asked about all controversial experiments and the answer is not simple. Should it be the scientists who know the most about their field? Should it be the government who make all the other laws? Should it be the people who this research will likely affect? Given that this doesn’t affect us at this time, it is not an issue that will be answered any time soon, but I am sure that it will be suitably sorted at which time it is needed.

Is it possible to prevent a disease without affecting other genes? Could there be side effects to doing this and is it acceptable to change other genes?

The answer to this varies depending on the disease being treated. It is likely the case that for diseases like cystic fibrosis and Huntington’s, where only a single gene is involved, that there would be and risk of involving other genes because it is only the one gene involved. This would not necessarily be the case for more genetically complex diseases such as Schizophrenia and Alzheimer’s, as multiple genes are involved in causing these. There are also environmental factors that affect the severity diseases like these and accounting for environmental factors as well as genetic ones is incredibly difficult. Another problem here is that we don’t know all of the genes involved with causing complex genetic diseases, as often there can be hundreds or even thousands! We are a long way off the possibility of having designer babies, but also far off being able to genetically prevent things like Alzheimer’s and Schizophrenia.

But what if they just grow babies in the lab past the embryos legal 14 days?

It is not possible to grow a full human baby in a test tube! We currently do not have the technology to artificially grow human babies; they need to be in womb in a person – we are far away from creating the Matrix, so worry not about it. If scientists do grow the embryos past the 14 days then they are breaking the law and will risk serious consequences for doing so. Real science has to be able to be replicated by other scientists; so if they grow the embryos past 14 days, they either have to lie about doing so in their work, or fess up, and risk serious consequences as previously mentioned.

You’re testing on human babies!

This is a valid concern held by many and one of the things that makes this kind of research so controversial is the introduction of human based testing. There is no answer here that will satisfy everyone and there never will be. I personally don’t view embryos and zygotes from the lab as humans, or potential human life. This is because they were donated by women, which suggests to me they don’t want them, and therefore children. Alternatively, they are the ‘left over’ embryos from IVF clinics, in which case they would be destroyed if the donor didn’t want to use them. I think the end justifies the means; no living, breathing, fully formed human is hurt by these experiments and the potential benefits in preventing genetic disease and miscarriages for future generations are limitless.

References

https://www.theguardian.com/science/2016/feb/01/human-embryo-genetic-modify-regulator-green-light-research

Mantikou E. Jonker MJ. Wong KM. van Montfoort, APA. de Jong, M. Breit, TM. Repping, S. Mastenbroek, S (2016) Factors affecting the gene expression of in vitro cultured human preimplantation embryos. Human Reprodiction 31: 298-311.

http://www.bdbiosciences.com/us/applications/research/stem-cell-research/m/1505552/techniques/intracellularstaining

https://embryology.med.unsw.edu.au/embryology/index.php/Embryonic_Development

Information about CRISPR

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

http://www.origene.com/CRISPR-Cas9/?gclid=CM2A2u-z3dICFUOdGwod4SEAeQ

The Basics of Genetic Testing

As many of you know the genetic make-up of an organism is DNA, but are you aware that it is possible to artificially copy DNA fragments using a process called PCR? Since its invention in the mid 1980’s, PCR has allowed many scientific advancements to come around quicker, and cheaper than ever before, which is great news for many scientists, including myself, as it is still one of the main genetic techniques used today.

What is the PCR and how does it work?

PCR stands for the ‘Polymerase Chain Reaction’ and is called so because it uses an enzyme called polymerase. To understand how PCR works it is important to understand the structure of DNA. DNA stands for ‘Deoxyribose Nucleic Acid’ and is made up of two main parts – a sugar backbone and nucleic acids base pairs. This is how it is named, the sugar that makes up the backbone of DNA is called a deoxyribose sugar. DNA is encoded by billions of base pairs: adenine, thymine, guanine and cytosine, each are denoted with the letters – A, T, G, and C respectively. I know this sounds a bit complicated, but bear with me, I have a diagram to help make more sense of it:

GDNA SEqune

As you can see, As and Ts are  always paired together and Cs and Gs are always paired together.

Despite only having four different bases, there are an unlimited number of combinations, because DNA is so long. DNA is structured in two strands which are stuck together by these base pairs (as shown in picture 1). All of an organism’s DNA is called its genome and the human genome is 3 billion base pairs long! Genes can be several thousand base pairs long, meaning that specific genes can be identified easily.

The next important thing to understand is DNA replication – how more copies of DNA are made. DNA replication is semi conservative, meaning that…. Actually, this is better explained in another diagram:

DNA semiconservitive

The red is the original DNA and the blue is the new DNA, showing how it is copied.

Okay, now we have waded through all that, we finally get to PCR and how it works.

PCR allows for the replication of DNA from a few base pairs to several thousands! This means that multiple copies of a length of DNA can be gained from a small starting sample in a matter of hours! This is how police are able to test DNA in small samples of blood found at crime scenes, PCR helping to fight crime!

For PCR to work we need more things than just DNA, this is where we get more technical again, sorry! The three important things needed are primers, a polymerase enzyme, and loose bases.
Important question, what are these things? Primers are a specific type of enzyme that attaches to the DNA and says “start replication here,” meaning that they determine how long the length of DNA you want to copy will be (because in PCR we normally only copy relative small lengths). A polymerase enzyme is the thing that attaches the bases together to make up the new strand of DNA. This is repeated several times, creating many copies because replication is exponential. This seems to also be best explained with my next diagram:

Cumulative DNA.png

With this in mind, what can be seen is that 30 repeats with just a single starting piece of DNA will result in over 100 million copies of the DNA!

There are so many uses for PCR, in  the case of police work as I have already mentioned and also for things such as paternity testing, as well as my Masters project. PCR is the main technique I am using to attempt to identify the gene involved which causes the different body colours of the snail Biomphalaria glabrata.

These are not pictures of my actual snails, they are quite small and somewhat hard to photograph, but I will try harder in the future.

But once the PCR has finished we need a way to see that it has worked, as sometimes enzymes don’t work or we forget to add one of the important bits (oops). This is where gel electrophoresis comes in as it always goes hand in hand with PCR.

What is Gel Electrophoresis and how does it work?

As the name suggests, a gel is made (not like a shower gel) it’s more like jelly (though I don’t recommend eating it). This is done using a compound known as agarose, which is a powder that is added to a liquid known as a buffer, and then heated to dissolve the agarose. It is poured into a mould which is rectangular shaped, with a comb at one end. This seems like it would be better explained with a diagram as well (I like diagrams, can you tell?):

The left picture is a basic representation, and the right image shows a gel I actually made. When the agarose solution cools to room temperature it will set in the mould shape with a jelly like texture.

A small sample of the PCR product is put into each well, as normally you do multiple PCRs at once. The whole gel is placed into a tank with more buffer, which completely covers the gel. This is where we move into a bit of biochemistry and physics, but only a bit, I promise. A current is run through the gel, which moves the PCR product through the gel. This is because DNA is negatively charged and is attracted to a positive current.

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This is what a tank looks like, it’s quite small, not like a fish tank or an army one at all really.

The moulded gel is left for about an hour and then put into a magic machine which can read where the DNA fragments have moved to within the gel. It ends up looking like this:

Once again, on the left is a representation and on the left is an actual gel picture from my Master project. Thankfully everything worked in this instance!

Project Introduction

I have created this blog to talk about my forth year project on snails, and also to look at things I have found interesting related to general biology and genetics. My aim is to write in a way that is understandable to scientists who are not specialised the field of genetics, and where possible allow information to be accessible to the general public.

For my master project I am looking into the molecular genetics of body colour polymorphism in the snail B. glabrata. This simply means that I am looking at the genetic differences in the body colour of these snails, as they can be either black or pink. Biomphlaraia are an important genus of snail to study as they are intermediate hosts for the human parasitic flat worm, Schistosoma. They are incredibly dangerous and can cause organ failure, infertility and in children, stunted growth and brain damage. I am looking specifically at B. glabrata because it has the most annotated genome of the all species within the Biomphalaria genus and one of the most common Schistosoma hosts.

The basis of this project is that it will hopefully be the first steps in reducing the prevalence of Schistosoma through the creation of transgenic lines of Biomphalaria which are immune to contracting the parasite. These individuals would then be released into area where Schistosoma are present and be allowed to breed with wild individuals, allowing for the spread of the resistance. Schistosoma resistance is a dominant trait and non-resistant individuals have lower fitness of the two. However, there is a long way to go before this is possible.

One problem to overcome in creating transgenic organisms is that success rates are never 100%, meaning that it is necessary to have a quick, inexpensive and easy way to identify individuals which have successfully have the transgene in their genome. This is where body colour comes in. For Biomphalaria glabrata there are two distinctive body colours – black and pink – where black is the dominant colour and pink the albino recessive and appears to follow a typical Mendelian pattern of inheritance. This is suggestive that albinism is likely caused by a mutation in a single gene, making it an ideal gene to target for the transgene, as disruption here will cause albino individuals, therefore making transgenic individuals easy to identify. The gene responsible for this is currently unknown and that is where my project comes in.

There are many components to this, but the first step is to try to identify potential genes involved. Using knowledge from other organisms, the current strongest contender is melanin causing the black body colour, which already gives many genes to look into, as the synthesis of melanin has many steps. Although this hasn’t been looked into in B. glabrata, it has been in many other species, and these can be used as references for potential genes in B. glabrata. Various genes involved in melanin synthesis are conserved between several species, particularly tyrosinase, which is involved at the very beginning of biosynthesis pathway.

melaninbiosynthesispathway

A simplified diagram of the melanin biosynthesis pathway.