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Fats, blood and DNA! Is there a link?

by YPU Admin on February 17, 2017, Comments. Tags: Blood, BMH, DNA, Fats, Genetics, PhD, and Research

Introduction

Hi, my name is Kathryn McGurk and I am a cardiovascular genetics researcher – I study DNA changes that lead to heart attacks and strokes. My PhD is with the Division of Cardiovascular Sciences here at UoM, funded by the Medical Research Council.



How I got here

At secondary school I loved Biology and Chemistry, and after working as a medical receptionist, I knew I wanted to be in healthcare. I studied Natural Sciences for my undergraduate degree at Trinity College Dublin, Ireland – a general sciences course which allows you to specialise in the last two years in a science of your choice. I joined thinking I would become a chemist, but fell in love with DNA studies and therefore specialised in genetics. My final year project was trying to find out what animal an unknown 8,000 year old piece of bone can from, using DNA analyses (it was a sheep!). After this project and work experience reading DNA for a breast cancer testing kit, I knew I wanted to do a PhD in genetics and aid in cures for disease.

In Depth

For my Ph.D., I use mass spectrometry to measure fats in blood. A mass spectrometer is a machine that can measure substances at really low concentration in blood. These fats are not like cholesterol, as they can kill cells, change the size of blood vessels, and cause pain. I am trying to find out if the levels of these fats in families with high blood pressure are passed down from parents to children through DNA. I will also find if their concentrations in blood are linked to DNA – if they are increased or decreased with changes in DNA. Changes in DNA change proteins which are formed from DNA. If a DNA change makes a protein which cannot produce a fat anymore, the fat might be at low levels in the blood of people with this DNA change, which could be good or bad for heart attack and stroke risk. I hope that by identifying fats which are important in cardiovascular disease genetics, they can be used to make new tests and treatments for heart attacks and strokes.

A typical month for me involves extracting fats from blood samples in the lab and running these on the mass spectrometer. I then go through the data the mass spectrometer produces and work out the concentrations of each fat in each family member. After some important data checks, I can use computer software to see if these fats are passed down through families and if DNA has a role in their levels in blood. I love how many different activities my work involves; lab work, mass spectrometry, and computer programming. Alongside research there is a lot of fun activities that I can get involved in – I am a student representative to help students with any troubles they have and I am a widening participation fellow, so I get the opportunity to teach A-levels students research skills and produce science workshops for students thinking about university. A PhD allows a lot of travel; I trained twice in Cambridge last year and I was given the opportunity to travel to Cape Town, South Africa this year to meet students there and learn more about genetics. With this Ph.D. I can stay in a university setting in the hopes of setting up my own lab someday, become a teacher, or work with industrial labs to help drugs being developed.

Going Further

Read: An obvious choice, but a great scientific read: http://www.nature.com/

Search: The Google of medical research: www.pubmed.com

Watch: David Attenborough’s Planet Earth II: https://www.youtube.com/watch?v=c8aFcHFu8QM

Study: http://www.manchester.ac.uk/study/undergraduate/courses/2017/00585/bsc-life-sciences/

More: Women in Science Blog: https://womenareboring.wordpress.com/

 

What is Graphene and what can it do?

by YPU Admin on January 31, 2017, Comments. Tags: graphene, PhD, Research, STEM, and UoM

Introduction

Hi, my name is Rory Brown and I’m in the second year of a PhD in theoretical physics. Specifically, I’m a part of the Graphene NOWNANO CDT at the University of Manchester, a programme that takes in students from all STEM backgrounds and trains them to do research in different areas of nanotechnology, mostly related to graphene and other similar materials – I use computer modelling to study how graphene behaves when we combine it with other materials to make electronic devices, and try predict if anything unusual will happen. I’ll tell you a little bit about what graphene is and hopefully explain why it’s so exciting, then what a PhD is like and how you can get there.


In Depth

Graphene was discovered here in Manchester in 2004, through an experiment so simple you can do it in 5 minutes at home. We start with graphite, the same material that we use in pencils. If you’ve ever held a piece of graphite, you might notice that it feels slippery and waxy – this is because graphite is made of layers of carbon atoms, organised in hexagons and stacked together like a deck of cards. Each layer is strongly held together but can freely slide over one another, and when you write with a pencil you break these layers apart, leaving some behind on the page. Graphene is a single one of these layers, and for a long time people argued that a single layer couldn’t actually be separated from the others, thinking it would be too unstable. It’s actually surprisingly easy to make – reaching in with a piece of scotch tape, the Manchester team was able to pull these layers apart over and over, until they finally had flakes of single layers of graphene, a material 10,000 times thinner than a human hair. Given that it’s only one atom thick we say it’s a ‘2D’ material, and since its discovery we’ve found a whole family of materials that can be made 2D.


Picture a: a sheet of graphene. Picture b: how graphene stacks are weakly bonded to make graphite.

So now that we’ve made it, what can graphene do? As well as being incredibly thin it has some remarkable properties, being incredibly flexible as well as the world’s strongest material: if you had a sheet big enough it would take the weight of an elephant balanced on a pencil to break through it! Industries are already looking into using graphene to make stronger, lighter materials for e.g. cars and aerospace travel. I’m interested in its electronic properties: electricity in graphene travels without any resistance, only 300 times slower than the speed of light, which gives it a lot of potential for energy-efficient electric devices.

One of the ways to make these devices is to combine graphene and other 2D materials, making thin sandwiches of different materials. What we’re left with is a stack only a few atoms thick, and the atoms in each layer can have different properties – one can be an LED, or a sensor. This is where I come in, making computer programmes to try and describe what happens in these layered materials. Working as part of this big group effort to improve our understanding of this new technology is very exciting and rewarding.

How I got here


My path to doing my PhD was fairly straightforward – I studied an MPhys in Physics here in Manchester, and my interest in graphene led to me staying. This isn’t always the case, and the NOWNANO CDT is a great example of how this can work: the people I work with come from a variety of backgrounds across all of STEM, some having spent time in industry beforehand. I’d love to continue with research, but there’s a lot of potential in PhD studies beyond that: you can go into scientific research or work in industry, or if that’s not your thing the skills that you learn (independent research, problem-solving, numeracy, presenting…) can lead to just about any job you can name. It’s a fascinating position to be in that’s full of opportunities all around the world.

Going Further

If you’re interested in some of the cutting-edge graphene research facilities that we have in Manchester, I recommend looking at the National Graphene Institute and NOWNANO websites:

http://www.graphene.manchester.ac.uk/

http://www.graphene-nownano.manchester.ac.uk/

The Museum of Science and Industry in Manchester also has an exhibit on graphene and other ‘Wonder Materials’ running until June 2017 that’s worth a visit:

http://msimanchester.org.uk/whats-on/exhibition/wonder-materials

Graphene also tends to pop into the news every now and then because of the promising factors just mentioned, so keep an eye on the science sections!


The National Graphene Institute.

 

City Space in St Louis

by YPU Admin on January 19, 2017, Comments. Tags: American Studies, City Space, Humanities, PhD, Research, St Louis, and UoM

Introduction

I’m Katie Myerscough, a PhD candidate in American Studies. I study part-time and work in Personnel at Marks and Spencer. I’m also a teaching assistant at the University of Manchester where I lead class discussions on American history, African-American literature and culture, and the southern United States. Like all busy students I prioritise my workload to meet my commitments; good time management is an essential skill to have at university and beyond.


How I got here

I went to the University of Oxford as an undergraduate and studied History. I was the first member of my family to go to university. After I finished my degree I tried a few different jobs; I’ve worked in museums, retail, and administration. I travelled around the world for a year and when I returned I started a Masters at the University of Manchester. I loved studying at Manchester, because it’s a very inclusive environment where I felt free to express my ideas and opinions, and I was supported to continue my own independent research into topics which interested me. American Studies is a very varied discipline, where you can study film, literature, politics, history and today’s society. Due to the really vibrant academic community at Manchester I decided to take the plunge and enrol for a PhD.

When I finally finish my PhD I will have a doctorate, which means that I will be Dr Myerscough and I can apply for jobs as a university lecturer and write books and articles about my work. I want to go into education of some sort, as I am fascinated by how people learn and how teachers can support different types of learners. 

In Depth

My PhD is about city space and how it can be used to convey and construct ideas about gender, class, ethnicity and race. The particular city I focus on is St. Louis between 1890 and 1925. This period in American history is loosely described as the Progressive era. Groups of reformers, politicians, business leaders, artists and journalists were worried about the state of the urban environment and the people who lived in them, so set about finding innovative ways to help American cities progress in a positive and healthy way. The progressive programs were interested in housing and schools, but also in the development of mass entertainment, fairs, and festivals.

Progressive policies almost always focused upon helping white Americans. During this time there was a massive amount of discrimination against African-Americans, and I look at how Progressive ideas could work to further that discrimination through segregation of city space.



To fully research St. Louis, the city plans, and Progressive programs created there I’ve visited the city and used the archives in its various libraries and universities. The archives I’ve used are very varied and include newspaper reports, maps, city plans, investigative reports, photographs and posters. Using archives is exciting because they offer a window into what people thought about the space they lived in, and how they tried to shape it.

It’s important to understand what people thought about urban space and how they demonstrated their hopes and fears for the places where they lived. Many of these fears are long-standing and are still around today. For example, why are certain areas of any city seen as dangerous? Why and how has that feeling been generated? Is it because there has been chronic under-investment in that area? Do the people who live there have the same access to schools, hospitals, parks and recreation as others? If not, why not? Asking questions about the city’s past can help understand its present and future.

Going Further

Here are some websites you may want to look at:

http://www.baas.ac.uk/  For the British Association of American Studies: great for resources and opportunities in American Studies in Britain.

http://www.baas.ac.uk/usso/meet-me-at-the-fair-the-native-american-model-school-the-philippine-reservation-and-maintenance-of-the-colour-line-at-st-louiss-worlds-fair/ This is something I wrote for U.S Studies online. This is a great forum for new writing from postgraduates and early career scholars. This piece relates to my work on race and ethnicity at the World’s Fair held in St. Louis in 1904.

http://www.mohistory.org/ This is one of the places in St. Louis where I did my archival research.

http://www.aaihs.org/blog/ For African-American intellectual history and great think pieces concerning contemporary events.

 

Applying Maths to Movement

by YPU Admin on January 5, 2017, Comments. Tags: Anomalous Transport, Applied Maths, Equations, PhD, Research, STEM, and UoM

Introduction

Hi! My name is Helena and I am a PhD student in applied maths at The University of Manchester. What that means is that after finishing my undergraduate degree in Physics, where I was taught a multitude of things about the world surrounding us, I decided I wanted to spend some time actually making discoveries for myself.

In Depth

There are hundreds (or even thousands) of equations out there describing ways movement happens; the movements which people observe all the time in experiments or real life are described by the so-called classical equations. Some of these you're probably already learning about at school.

What I do now is study what we call “anomalous transport”, which basically just means movement that somehow looks odd or unusual.  The equations for anomalous transport differ from the classical ones in that they in some way or another require `memory effects' in order to fit experiments. The scientific principles teach us that experiments must always be the starting point of any work we do: we build theories to fit the data, not change the data to fit the theory we already have. And so that's what I do. I try to find mathematical descriptions of the kinds of movements scientists working in e.g. biology see in the lab. Once I manage to find a good fit between my theory and the data they gave me, the experimental scientists can then go away and do more experiments to test the predictions of my models.

Of course it's not just my model, but that of my entire research group. Depending on how difficult a problem is, it can often take several of us to solve it. An example of such a problem is intracellular movement, so movement that happens inside of the cell. For example, researchers in biophysics and biology are interested in how essential nutrients are transported from the nucleus to the cell membrane. This transport happens partly through the work of “motor proteins”, and the movement of these inside the cell are known to be anomalous. An image of how the transport happens is shown below.


Drawing 1: The picture shows a motor protein (brown) moving a cargo (blue) along a microtubule. Microtubules are pathways to transport nutrients across a cell. 

When you think about all the different parts of a cell, and the processes that happen in it, it is not very surprising that the equations one would need to describe this kind of transport would have to be rather complex. In particular, what we find is that the movement you see any point in time will likely also depend on what happened a while ago. For example, if there are several motor proteins all moving on a microtubule they might cause some kind of `traffic jam', which will affect the motors for a while until the path becomes clear again. This, and many other things, can be the cause of `memory effects' in our equations so that we may have to account for all movements up until the point we're looking at in order to predict how the movement will continue.

While this makes the work harder, it is very important in understanding what might cause transport in cell to stop happening, leading to cell degeneration. This is linked to various neurodegenerative diseases and could potentially be instrumental in designing better medications.

Other examples of where you might see this kind of anomalous movement include the flights of bumblebees in a field, sharks hunting for prey in the ocean, and even the optimal part a robotic vacuum might take across your living room floor!

Going Further

If you're interested in learning more about anomalous transport, our research group has a website with more examples.

http://www.maths.manchester.ac.uk/~sf/anomalousdiffusion/index.html

Otherwise, if you want to learn more about intracellular transport there is a very useful introduction here:

http://www.studiodaily.com/2006/07/cellular-visions-the-inner-life-of-a-cell/

Finally, if you want to get an idea of all the other amazing areas maths can be applied to you can visit

http://www.maths.manchester.ac.uk/our-research/research-groups/industrial-and-applied-mathematics/

 

Understanding and resolving economic inequalities in the North of England

by YPU Admin on December 8, 2016, Comments. Tags: Humanities, North of England, Planning, Research, and UoM

Introduction

My name is Tom and I’m in the first year of an ESRC-funded PhD in Planning at the University of Manchester.





How I got here

I went a bit of a roundabout route to get here - certainly not a conventional path to doing a PhD. I did my first degree in History and Politics at the University of Sheffield, finishing in 2006. I then went on to work in political relations and policy for a host of different organisations and clients, which involved talking with politicians, the media and the general public about various issues. Some of the projects involved working with developers on new housing, shops, offices and energy infrastructure…which is how I became interested in planning.

At the same time, I was becoming increasingly interested in the economic disparities between the North and South of England. As someone who has lived in the North for most of my adult life, I wanted to understand more about why much of our region seems to be struggling economically, and what we could do about it. So, in 2014 I decided to do a part-time MSc in Urban Regeneration and Development at the University of Manchester, which combined my interest in planning with a focus on local economies and what you might call ‘place’ issues - what makes a city or town a good place to live, work and play? Soon after starting my MSc I decided I was enjoying research so much that I wanted to do more of it, so started a PhD titled Sustainable Spatial Rebalancing for Northern England: Alternative Models and Future Scenarios in September 2016.

My PhD is co-sponsored by IPPR North, a think tank based in Manchester who do lots of fascinating work on how to improve the Northern economy. You can find out more about what they do here: www.ippr.org

In Depth

Interest in rebalancing the UK economy isn’t new. A wide range of policies have been tried over the last 100 years, yet huge economic inequalities exist not only between the north and south but within Northern England itself. Manchester, for example, has been hugely successful in creating jobs in the city centre and making the city a much more attractive place for businesses to invest, yet just outside the city centre are some of the most deprived parts of the country. My research involves understanding why these economic inequalities exist between places and how these problems might be resolved.

I’m in the first year of my PhD, so a lot my time is spent reading what others have written on this issue, and trying to formulate my own ideas about how we can make the North of England a more economically successful place. I also try to spend plenty of time out and about, visiting different parts of the North to try and understand which policies are working well and which aren’t. Aside from that, we have lots of training. Methods training is a big part of being a first year PhD, as we start working out how we’ll be carrying out the main part of our research from second year onwards.

We have a really vibrant and varied group in the School of Planning and Environmental Management here at Manchester, which includes people from all over the world studying various aspects of planning, urban design, architecture and environment-related subjects. With so many different perspectives on how we see the places around us, it’s a really interesting department to work in.

Going Further

You can read my blog about my research and other related interests here: https://tomjarnolduk.wordpress.com

I’m also on Twitter: @tj_arnold

For more on the School of Environmental Management at the University of Manchester: http://www.seed.manchester.ac.uk/planning/