This ain’t a scene, it’s a Goddamn arms race – the war against antibiotic resistance

Originally posted on allinthegenes:

Bacteria. Eurgh. Microscopic bugs that we can’t live without. Icky as it is to contemplate (or amazing, if you’re one of those microbiology-fetishist sorts like Mr AllInTheGenes) the human body is home to bazillions of bacteria. That’s right, bazillions. On our skin, in our guts, in our mouths (eurgh eurgh), we wouldn’t function without these tiny troopers. The yoghurt adverts call these our ‘good’ bacteria. But for every Luke Skywalker there’s a Darth Vader — getting infected with ‘bad’ bacteria can cause food poisoning and meningitis and septicaemia and pneumonia and… you get the picture. What’s more, even the good bacteria can turn against us, Anakin Skywalker style, if they find themselves in the wrong part of the body, or if something happens that gives them an advantage over their neighbours. At the moment, we combat unwanted bacteria with antibiotics: compounds that stop the bugs from functioning properly. But as…

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The story of your life before you’re even born

This was a piece I wrote for a competition under the question of “why is your research important?”. It didn’t win or anything but I really enjoyed writing it and thought it might be a nice read so have now put it up here…

 

 

Over 3 billion molecules describe who and what you are. They are a combination of just 4 different types of molecules abbreviated to A, G, C and T. Those 3 billion letters are your book, and my research is to read it and understand it. This book is your genome and the letters are a representation of your DNA. Some of it already makes sense to us, for example about 2% of it is your genes and codes for proteins. However, that leaves a vast portion of ‘gobbledygook’, letters strung together in illegible sentences or in a language we don’t yet recognise. This is where I’m searching for meaning.

 

If the majority of your DNA isn’t your genes and doesn’t code for proteins, then why is it there? My research takes me into specific regions of your DNA scattered throughout your genome that are almost identical to other non-coding regions of DNA in chick, mice, fish, sharks, frogs and near enough every vertebrate organism that has had their DNA sequenced. This similarity doesn’t seem like a coincidence so my lab is trying to unravel the functions of these conserved DNA regions.

 

It just so happens that these conserved non-coding elements (CNEs) lie near genes that we know are important in early embryo development. It is because of this that we think the CNEs could affect, control and regulate the developmental genes. Therefore we believe that these conserved non-coding regions of DNA are important for the regulation of the vertebrate development system. My personal research specifically looks at what happens when this process goes wrong.

 

Development of the embryo is such an intricate process with many steps. A whole field of science is continually working out what cells divide and multiply where and how to turn a single fertilised egg into a whole organism. In vertebrates, there is even a stage where the embryos of a chick, mouse, fish, shark, frog and even human look incredibly similar. This further makes us believe that these non-coding regions of DNA that are the same in all of these organisms contribute to controlling the similar development processes. As development is so intricately controlled, the slightest changes in these CNEs could impact the development of the organism in detrimental ways.

 

All of our DNA can potentially have mutations. We can inherit these from our parents or they can be newly acquired ones specific to us. If these CNEs have mutations, could this affect their function and could this cause people to have developmental disorders or anomalies? We don’t know yet, but I sequence the DNA of people in an attempt to find these anomalies and pin down what effect they may or may not have.

 

So many parents have children with developmental disorders and are left without an answer to why. If we can’t find any mutations in the genes, we have to extend our search beyond them, to the ‘gobbledygook‘ strings of As, Gs, Cs and Ts in between the sentences we understand. Trying to find meaning in something that makes no sense to us is a difficult process. I spend a lot of my time sifting through potential variations in the DNA of these children and their parents looking for something that could potentially explain the so far unexplainable. Once a list of potential candidate mutations are found, we have to try and test the theory that they are involved in controlling the genes nearby and that this mutation causes the change in control and contributes to these developmental disorders.

 

We all have our own DNA, our own books. For many of us, we live our lives not knowing what it says but that doesn’t matter because we live healthy lives. However when things go wrong we have to turn to it to work out why and whether we can do anything to help. Science research is always stepping into the unknown, that’s how progress is made. However daunting the task of searching the remaining 2.94 billion letters for a new language may seem, understanding our genome in its entirety is essential to understanding why things can go wrong and how to treat, help or even prevent these genetic disorders.

 

My research matters because your DNA is your story, and some of the most important parts are already read before you are born.

The King’s College London scientist purge: what message does it send? | Jenny Rohn | Science | theguardian.com

The King’s College London scientist purge: what message does it send? | Jenny Rohn | Science | theguardian.com.

I’m saddened to hear that this is happening at my old university, a place where I was proud of the attitude shown to research. In addition, King’s has been falling down the league tables thanks to shoddy student satisfaction and I hardly think something like this, which will drastically affect quality of teaching and even increase class sizes, is going to help that situation.

Science students, lecturers and researchers at universities like King’s stand side by side and build relationships based on excellent work and trust. The university is not showing any of these groups of people the respect they deserve and has annihilated any trust between themselves and their own scientific community.

Please show your support of the King’s staff and sign the petition here: http://www.change.org/en-GB/petitions/rick-trainor-stop-kcl-health-school-redundancies

 

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Facebook “mind control” isn’t new

It’s all over the news, and it’s not looking good for Facebook and the researchers behind a newly published study. In case you haven’t heard, Facebook has teamed up with a group of researchers and manipulated the emotions of almost 700,000 of you during a week in January 2012 (http://www.pnas.org/content/111/24/8788.full). The paper describes the occurrence of ‘emotional contagion’ where people exposed to more positive posts on their news feeds post more positive things themselves and vice versa for sad posts. However this shouldn’t come as a surprise. I’m not saying the results are unsurprising, I’m saying that Facebook has manipulated your newsfeed to get an emotional response, and you shouldn’t be surprised.

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http://www.phdcomics.com/comics/archive.php?comicid=562

The P word

Scientists both fear it and get excited goosebumps over it, but it’s not easy and it’s not quick. Publishing. Getting your work to a stage that’s ready to be seen by the masses, criticised by many and cited by whoever thinks it’s important.

 

I may only be a first year PhD student but already publishing my work is something I have to think about. It’s not like I’m even having delusions of grandeur as my boss has mentioned the P word to me many times now. I may not be first author on a (hopefully) near future paper but contributing is a massive step for me and fills me with excitement.

 

Before I started my research, I had very little knowledge of how publishing your work even worked. Now I’m a little wiser and have uncovered a dark, complicated route to getting your work seen. Here I outline a few of the things I’ve learnt…

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Sciencey stuff from a PhD student

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