Celebrating Ada Lovelace: Female computer scientists at Roslin
Computer models to investigate Salmonella, anti-inflammatories, microbes, animal health and genetic differences between men and women.
To celebrate Ada Lovelace Day, a number of female computer scientists at The Roslin Institute describe how they use computing and bioinformatics skills for investigating biological processes in animals and humans.
Dr Prerna Vohra on fighting Salmonella
There are over 2600 types or serovars of Salmonella. Some of these survive within farm animals cattle and spread to humans via contaminated meat causing human infections. But many types cause disease in farm animals too. Before we can design vaccines and control measures to limit Salmonella in farm animals and minimize the risk to humans, we need to understand if some of types are better than others at surviving within these sources.
By using bioinformatics tools to analyse the genomes of Salmonella serovars, I found genetic signatures that are unique to each type of Salmonella. By looking for these signatures in mixed populations of Salmonella, I can identify exactly which types are present in the population and can infer their fitness by how much of each type is found. Using this method in cattle, I found that all the serovars we tested survived within the bovine lymphatic system and thus, pose similar risks to humans.
I am hoping to explore the usefulness of this method to test how effective vaccines and interventions are against different Salmonella serovars and also for the routine surveillance of farms, food products and the environment, which can contain several types at the same time, and perhaps expand it to study other bacterial infections.
Dr Barbara Shih on anti-inflammatories
As we age, our immune response gets worse at fighting off illness, which could be caused by low level background inflammation. I am studying whether anti-inflammatories will improve the immune response in elder individuals by looking at their response to vaccine before and after treatment.
I use computational analysis to study the small changes that anti-inflammatories might have on the body by looking the gene expression.
Dr Laura Glendinning on the role of microbes
I research the microbial communities which live inside of various livestock species. These communities are known as microbiota and they have a large impact on animal health, nutrition and wellbeing.
Traditionally the way in which we would research these microbes would be to grow them in the lab. However, lots of microbes can’t be grown in this way. By using software to extract and sequence the DNA from these microbial communities, I identify what kinds of microbes are present and I can also begin to work out what role they might have in the animal they are inhabiting.
Amanda Warr on animal health & disease
Every living being has a four-letter DNA code. I use special equipment called a DNA sequencer to read fragments of DNA. To help me make sense of the code, I can use computers to overlap these fragments and piece the DNA back together so I have the full set of DNA, or the genome, of an individual.
Once that is done, I can use sequencing data to do things like compare individuals to figure out what differences in the DNA of the animal, or the DNA of microorganisms living inside the animal, make some individuals healthier and more productive than others, or I can look at the genomes of viruses to track how they spread through populations.
Elena Bernabeu Gómez on genetic differences between men and women
As a PhD student at The Roslin Institute, I’ve delved into the world of bioinformatics and quantitative genetics following an undergrad in Biotechnology, using computational tools to bring light into how our genes and environment lead to the human traits that make us unique.
My recent work has focused on genetic differences between men and women, looking into how the same genetic code could potentially lead to different consequences in our bodies, ranging from differences in body measurements to disease status.
With this effort, we hope to further understand the workings of genotype-phenotype connection and possibly make a case for improved precision medicine between the sexes.
Dr Christelle Robert on genomics for resilience to environmental stress in livestock species
My group is interested in what makes animals resilient to environmental stress, tropical parasites and diseases. Within this theme, I am exploring the interplay between low quality diets and the gut microbiome in livestock species in the context of harsh tropical environments where animals are fed sub-optimal diets.
After extracting and sequencing the DNA from the animals' gut content, I use bioinformatics software to mine sequencing data and assemble the genomes of microbes to help in deciphering their roles in animal productivity and resilience to stress caused by feed scarcity.
Becky Smith on the DNA of microorganism in the cow gut
DNA is the code of life that is stored within living things, from large trees to tiny microorganisms. Studying this DNA allows scientists to learn a lot about living things, such as physical or behavioural characteristics, or how closely related they are to each other. We can look at how related individual species are by imagining them in a tree of life, much like you would consider a wolf and a dog to be more closely related than a wolf and a whale.
We use computers to look at the DNA present in an environment such as a cow’s gut, and determine which microorganisms live there. We call this a metagenome, as it encompasses the DNA, or genome, of all living things present. Sometimes, we cannot tell which microorganism the DNA belongs to, as it may not have been seen before. Using a technique called metagenome assembly, we can use tools on a computer to join the DNA into individual microorganism genomes. The focus of my PhD project is to investigate bioinformatic methods of metagenome assembly. We hope that by knowing more about the DNA of microorganisms that live in the cow gut, more can be learnt about the impact of the microorganisms on methane emissions, food production and animal health.