Hi, my name is Emily Perry and I'm a scientist. I work at a place called EMBL EBI, which stands
for European molecular biology laboratory, European Bioinformatics Institute. That first
bit the envoy part shows we are part of a large organisation with lots of different
centres in different countries. The second part EBI is specific to where I work. So let's
take a minute to unpick what that means. Firstly, we European, which means we're an international
organisation. We get funding from all over Europe and we have people working here from
all over the world. There are huge amounts of international collaborations in science.
Secondly, were the bio informatics Institute. What do you think that bio informatics means?
Can you break the word up into parts? Teachers, you may wish to pause the video for a moment
to discuss bioinformatics means we study biology that's the bio part using computers. That's
the informatics part. Bioinformatics is a great way to do scientific research without
working in a lab. Lab work requires a lot of specialist equipment and reagents. For
bioinformatics, you just need a computer with access to the internet. Sometimes we do bioinformatics
to help with lab work, we can use public databases to decide what to experiment on. And then
we do the experiments in the lab and analyse the results with a computer. However, some
researchers work only on bioinformatics, creating tools and databases and analysing data. To
do this kind of work, you have to understand the science behind what you're studying. But
also have the computational skills like coding to do the analysis? What benefits can you
think of for using computers to reserve living things, rather than relying on lab experiments,
teachers may be paused for a moment to discuss. Things you might have discussed could include
flexibility of when and where you can work, reducing animal testing, reducing costs of
research, saving time, and being able to process and analyse huge amounts of data, what we
call big data, you might have come up with your own ideas to today's practical is something
that real scientists would do. We're going to investigate a gene to find it in new species.
Researchers might do this to help them design experiments to do in the lab, or they might
have identified a gene from experiments and want to know more about it. Before we get
stuck into the science, I'm going to tell you a little about me how I ended up in the
job I do and what working for a large science organisation is like I went to an ordinary
comprehensive school in Lancashire. I did sciences for GCSE and A level, but I also
did a bit of drama. Then I went to the University of Edinburgh, where I studied genetics, then
I stayed on a data PhD, a Ph. D is another degree that you do after your undergraduate
degree. During a PhD, you work on a long term research project. Mine took three years, then
write a thesis at the end. For science PhDs, you often do these in a lab. It turns out
that I'm terrible at lab work. I am clumsy, and I am impatient, which are not good in
a lab. But I did a lot of science communication stuff alongside it, which got me a job doing
science communication in schools. These communication skills got me a job at EMBL EBI, doing outreach,
which means I teach and train scientists how to use the online resource called Ensembl
that you're going to be working with today. I now manage a team doing this, which means
my job title is on symbol Outreach Project Leader. My job is really cool, because I get
to work with new and exciting scientific data. So I'm always learning new science and finding
out about the research that's going on. I also get to travel to research institutes
around the world to teach courses. So I'm always meeting new people learning about the
science they do, but also about their cultures.
Although I work
in bioinformatics, I didn't study it. When I was studying bioinformatics was quite a
new subject. So you couldn't really study it at university and a lot of a lot of the
skills I need I picked up on the job. This has changed a lot. And now you can study bioinformatics
at undergraduate level or masters. There are even apprenticeship type programmes part of
my job involves working with new research projects like Darwin Tree of Life. Darwin
Tree of Life aims to sequence genomes that's full DNA codes for every species in the British
Isles. We wanted to use this project to let you know about what's happening with the Darwin
tree of life, and how the data it produces helps us to understand evolution, and the
different types of species in the British Isles. We also wanted you to see a different
side of scientific research using computers. And if any of you are keen on computing and
science gives you a glimpse of a potential career you might want to go into. All species
on Earth came about through evolution, we all descended from a common ancestor with
different organisms adapting to different environments and lifestyles. We can see this
when we look at the morphology of different species, comparing the shapes of their bodies,
and how they use them. Here we can see vertebrate limbs, and how they all evolved in the same
bones. But these bones differ in shape and size, to allow them to function in different
ways, such as hooves, fins or arms. Can you see which bones are the same and how they've
changed? Teachers? Let's pause the video and take a look. morphology is how scientists
have studied evolution for hundreds of years. It was how Charles Darwin came up with his
theory of evolution by natural selection. But in the last few decades, scientists have
found a new tool for looking at how species evolve. We can see evolution when we look
at the DNA in different species, and how the sequences of genes change. This is where bioinformatics
come in. A gene is a sequence of DNA in an organism's genome. The precise order of bases,
A, T, G and C, determine the precise order of amino acids in the protein it codes for.
The amino acids allow the protein to fold into its correct shape, and carry out its
function. During evolution, the sequence of a gene and its protein change genes which
started out the same and diverged or changed over time between species are called orthologs.
For example, the gene I worked on during my PhD is called nip bl, and is involved in holding
replicated DNA together until it separates at mitosis. It does it in the human cells
I was working with. But a lot of what we know about this gene comes from studying the orthologue
nipt be in fruit fly. The sequence of the gene is similar, but not identical between
human and fruit fly, and it does the same job. What uses Can you think of the studying
orthologs we can pause the video here to have a discussion. We can identify functions of
genes by finding their orthologs. In other species, we can study changes over evolutionary
time, we can find functional regions of protein. Darwin Tree of Life aims to sequence the genome
of every eukaryotic species in the British Isles and the surrounding seas, we can find
the genes in these genomes by sampling the RNA. When genes are expressed, the DNA is
copied or transcribed. To make signal molecules called RNA, we can sequence the RNA, then
use sequence matching to map the sequences onto the genome. This tells us where on the
genome the genes are. This can all be done using specially designed computer software.
Once we found the genes, we then have to work out their function. And this is much harder.
extensive work by biologists is needed to carry out experiments to see what a gene does.
This can involve seeing what happens when the gene is mutated, visualising where the
protein is expressed, and finding what other things in the cell the protein interacts with,
and much more. This is very time consuming. However, a lot of work has already been done.
We know the function of most human protein coding genes, partly by studying them directly,
and partly by studying them in orthopaedics, or the equivalent genes in model organisms,
such as mouse, yeast and fly. This is down to 1000s of scientists working on this over
many decades.
orthologs usually do the same job in different species. Both the human gene I worked on nipa
B L and its orthologue nipt. B and fruit fly are involved in holding DNA together after
it wreck replicates. So if we can find the orthologs of newly identified genes, we can
find what they do. In this way we can use bioinformatics to drastically reduce The amount
of experiments we need to do. For example, I was working on nippv l in human because
someone found that it was linked to a genetic disease. Because we already knew that in the
fly nippv was involved in holding the DNA in place, I could focus my work on looking
at where the DNA was held in cells with this genetic disease. Finding orthologs involves
matching sequences. One algorithm that is a computer process or programme that can be
used to match sequences is called blast, which stands for basic local alignment search tool.
Blast takes a short sequence, and tries to find were in a longer sequence such as a genome,
or set of sequences such as all the genes in the genome, it matches, blast assign scores
to match is it confined and gives the highest score to long matches with little to no gaps.
You can run blast with either protein or DNA sequences. Now let's try a practical with
this blast tool.
Today, you'll be using the same website that researchers use, and it is open to anyone
to use wherever they are in the world. Ensembl is a website and database where researchers
can find information about genes, genomes and proteins. well studied genomes such as
human can be found on ensembl.org. There's loads of extra information on the genes like
what they do, what effect changes in the genes have and where in the body the genes are expressed.
species which are not so well studied, such as the genomes being sequenced as part of
Darwin Tree of Life and a very new are being put out speedily, with minimal extra information
on rapid.ensembl.org.
In this practical, you're going to find the human gene and export its protein sequence,
then you're going to use blast to find the same gene in some of the Darwin Tree of Life
species. Pause the video here and refer to your worksheet for instructions on this practical
the sequence of genes and proteins change incrementally over time, which is what evolution
is. Lots of these changes put together cause the major differences we see between species.
By comparing related species, we can work out when changes occurred in evolutionary
history. This can help us to categorise newly identified species.
We can also work out when species diverged and why we do this by aligning sequences together.
One algorithm that does this is called cluster cluster uses similar scoring methods to blast
but it can group together lots of sequences and say which ones are the most similar to
each other. Now let's use Clustal in another practical
we can use the sequences of the human sea otter, Black Swan and Atlantic cod genes that
we found in the last practical in the next one, we need to export these from ensemble.
We will use cluster Amiga to align new sequences together. cluster will group sequences based
on similarity and also allow us to see regions that are common to all the proteins. Pause
this video and refer to your worksheet for instructions. In this activity, we've used
a real database that scientists use in their research. As you saw all the data is publicly
available. And it can be accessed by anyone with a with a computer and an internet connection,
including you. This is called Open Data and is a cornerstone of bioinformatics research.
We use this database to find a gene in humans that had already been studied. We use the
sequence of the human gene to find the same one in other species, which we know a lot
less about. We looked at how these genes are different to each other and why they are different.
This is the sort of analysis the science that scientists might do before starting to run
experiments. This allows scientists to find out as much as they can about a genie, just
a few Minutes. As a result, scientists may be able to develop cures for disease or contribute
to conservation efforts. If this activity has sparked your interest, you could try investigating
other genes. You'll find lists of human genes on places like Wikipedia that you could search
for. You could also try finding the same genes in other species that we didn't look at in
these practicals. You may be the first person in the world to explore these genes. Remember,
you don't need to work in a lab to be a scientist. Bioinformatics is a rapidly growing area of
biology, and will be vital in solving some of the world's biggest challenges, from adapting
to climate change to finding alternatives to oil based products to conserving our most
valuable and endangered species. If you want to know more about a career using computers
in biology, go to your genome.org or search for a bioinformatics degree University
Transcribed by https://otter.ai