A warm wecome- Week 1
Welcome to
Antibiotics Unearthed!
...And welcome to my
blog!
This is my personal
blog, sharing my experiences as a student actively taking part in the
Antibiotics Unearthed research project. I aim to provide readers with
a week-by-week summary of what we are doing, what we find, and what
we aim to achieve in the lab as we progress on our journey with this
exciting initiative at the University of Westminster.
So what is
Antibiotics Unearthed and what is all the fuss about?
In a nutshell, the
main aim of Antibiotics Unearthed is a biodiscovery project. The aim
is to observe taxia of marine bacteria as potential sources of
compounds to help us overcome antimicrobial resistance, a growing
public health concern. On a larger scale, Antibiotics Unearthed is a public engagement venture fronted by the Microbiology Society.
Week 1: And so it
begins… bright eyed and bushy tailed students listen intently as
the project begins.
This week brought
together applicants from a broad spectrum of enthusiastic students
from different disciplines within the Life Sciences for this exciting
cross-university research project. I had worked hard on my statement
and I knew how much of an impact this project could have globally to
combat the challenging global threat of antimicrobial resistance so I
was delighted to be involved despite understanding the scale of the
task at hand early on.
I quickly realised
that the level of individuals involved in the project is quite
impressive, and spans over Foundation level study all the way to PhD
level with subjects ranging from Biological Sciences to Biochemistry,
Pharmacology, and Nutrition. This was no accident. We have at our
disposal a melting pot of specific skills and talents to add to the
project as integral parts of a whole. I feel it is always important
to look at things from different perspectives and from different
angles so I welcomed this and became curious as to what each
individual could bring to the table (or lab bench).
As we split into
separate groups it really brought it home just how much of a team
effort this is going to be, and it feels good personally being able
to contribute with your own unique skills set to benefit the project
as a whole. It gives each individual value, we are not just here to
make up the numbers and each individual’s unique skills set will be
valued and will be a great asset to the project. For me, this is what
university is all about, and it is why I am here. I want to make a
real, tangible difference with my work and my research, and to be
able to do this on such a large scale would be quite humbling for me.
As I say, it is
important to approach this type of research from a variety of angles,
and this was impressed upon us early on. Each member of the team
therefore can provide unique insights to the project, from our
culturing methods, methods of results and interpretation of those
results. This can also provide use for overcoming eventual stumbling
blocks as we progress.
Lessons from
IGEM…
We received a talk
from the International Genetically Engineered Machine (IGEM) team at the university about their research into
Biofilms and antimicrobial resistance to give students a taste of
this type of work and what is involved, how to succeed, what to
expect, what to do, and importantly what not to do!! It gave us a
flavour of what this type of extracurricular work could look like.
Expect to ‘fail’
on your way to success..
This could actually
be said about many things in life. In terms of this specific type of
research, we were reminded of this important lesson by the IGEM team
at the university, who stated in their presentation about their own
research that bacteria is unpredictable and so it doesn’t always
play ball. It doesn’t always do what you think it will or want it
to, as with most lab work, but more specifically in this instance.
The main
introductions from some rather important people at the university…
Dr. Linda Percy, head of this project at the university, began her
presentation by exclaiming that she is incredibly excited about this
nationwide initiative, matching the students palpable enthusiasm when
stating.:
‘ I have been at the university for probably about 11 years now and
I don’t thinkk we’ve ever done a project like this before in the
time that I have been here.’
 |
| Dr. Linda Percy heads the project at the University of Westminster. |
Dr. Linda Percy is a marine biologist, working with single celled
organisms- eg. flagellates
She is not a true bacteria microbiologist, but her interest in
bacteria initially came from doing some electron microscopy on the
south coast.
She became interested in research concerning very large celled
organisms- prorocentrum lima. They are of interest as they contain
a toxin that can give people diarrhoea, which is clearly not a very
pleasant experience and not what we want. If shellfish eat these
cells they accumulate a toxin as a result if people eat the shellfish
they become very ill and spend a lot of time on the toilet.
Her main interest was trying to identify these cells, looking at growth plates and observing pore patterns. The pore patterns are used to identify the different species of interest. Electron microscopy was applied using a scanning electron microscope and these are some of the impressive, detailed images that result, looking down the microscope.
She didn’t only see the presence of these cells, but you could also
see that living on the surface of them were a range of spirochete bacteria, rod shaped bacteria, and some biofilm as well. A lot
more going on and potentially very significant!!
Dr. Percy was clearly explaining to us, through her own extensive
research in this area, that with marine bacteria nothing is usually
of importance in isolation alone. Bacteria works in concert with each
other to produce these actions and effects, which is also an
important factor of why it is so notoriously difficult to grow marine
bacteria in the lab, despite the use of novel techniques in order to
make use of the huge potential for these microbes to aid us in our
fight to combat antibiotic resistance.
Dr. Percy reminded us of the fact that these microbes are not only
living on their own, but are living in this community (‘taxa’) of
other organisms. She went on to explain that this is how she started
to get interested in marine bacteria. The beauty is actually in the
complexity of it all.
Dr. Percy impressed upon us, from this example, that when students
have worked on this in lectures over the past few years looking at
trying to identify some of the microbes associated with these
bioflagellates- that one of them provoked particularly special
interest as it can produce polyhydroxyalkanoates (PHAs)- which is a
biodegradable plastic which the university has been working on
recently. PHAs are promising candidate for biodegradable polymers despite its relatively high production cost. Theoretically a higher demand for this material as urgency for its use rises may help to bring costs down.
 |
| Microbial production of polyhydroxyalkanoates (PHA) (Anjum et al., 2016) |
This potential of this discovery is huge if it can be successfully used to purify our oceans. It is no secret how contaminated our waters have become with these plastics. Solutions are of urgent need so this research has impact on a global scale for not only food production, but also animal welfare and public health outcomes. Certainly fascinating uses of biotechnology from the university here. It is vital that we get a better understanding of the mechanisms of PHA synthases in order to develop better polymer production strategies.
It is crucial to understand the mechanism of these enzymes in order to develop better polymer production strategies. Dr. Percy went on to explain the complex systems of how this work in
line with the endogenous clocks of these organisms in an ingenious
cycle that would be beneficial both for the host and potentially
humanity and sea life as a whole, cleaning up our waters.
 |
| An estimated 6-12 million tonnes of plastic enters the oceans each year (3), wreaking havoc on marine species. The toxicity continues to worse. Could PHAs help us to overcome this alarming trend? Image src: http://www.businessinsider.com/plastic-in-ocean-outweighs-fish-evidence-report-2017-1 |
Every new
beginning comes from some other beginning’s end...
Back to specifically talking about this project. Dr. Percy explained
how her excavations across the UK coastline will benefit our research
we will be undertaking in the lab.
Over the years Dr. Percy has been around the coast collecting many
different sediment samples- in boats, excavating the shoreline,
harbours, grabs over walls, and on foot in wellies!
Sediment was collected all along the coast, from north to south to
look for interesting samples. This has been going on for a fair few
years now and these sediments have all been stored away, thinking
there would likely be a good purpose for investigation some day!
 |
| Image courtesy of Dr. Linda Percy. |
We were presented with a practical example of how samples could be
used from research of a PhD student who was at the university from
Kazakhstan. Kazakhstan unfortunately has high oil pollution. It was
fascinating to hear applications from sediments to scavenge toxins
and learn how to find methods to look for marine bacteria in marine
samples without getting too frustrated by poor results. This PhD
student had been working hard to develop a method of seeing what
species of marine bacteria could naturally degrade hydrocarbon. I
look forward to hearing more about this research but I know these
things take time. This is an important lesson.
 |
| How tiny algae cultivate oil degrading bacteria. (3) |
There’s method in the madness…
Some techniques, such as Next Generation Sequencing, were briefly
introduced and outlined to analyse these sediments from the UK.
We discussed how molecular techniques were used to observe less than
1g of sediment to try and determine which species are useful and just
how much of a HUGE array of different bacteria was in these sediment
samples.
2 different samples were identified as being of special interest- One
from Orkney, at the very top of Scotland- and one from Ramsgate in
Kent, on the south east coast of England. With these 2 samples alone
we have a huge array of different bacteria to observe. Crucially, we
can observe how the different bacteria within these samples may be
reliant upon each other, and what materials they require for survival
and growth. The foundation of this information that has been building
up for quite some time now will provide us with the information we
need to begin the Antibiotics Unearthed project at the university.
Reality check…
It is not necessarily the case that all of these will be cultural. In
reference to the paper we were set to read in preparation for this
lecture, we learned the finer details of how these bacteria work in
association with one another. As such, one of them may grow and
produce something which another of the bacteria population requires.
The teamwork
makes the dream work...
For the groups we were split up in different levels and there were
groups of 4-5 with a total of 9 separate groups. This is because some
will undoubtedly have better skills in microbiology compared to
others and some generally have more experience in the lab.
After exchanging pleasantries and getting to know each other better,
we were quickly set a group task to see how we could work together,
communicate effectively and introduce ourselves to the material,
familiarising ourselves with our given antibiotic to study in depth
and then present to the class.
We all seem to be ‘leader’ personalities so we quickly set up a
watsapp group and delegated roles to ourselves from the task
instruction on areas to focus on. This naturally evolved into a
democratic process rather than a Lord of the Flies scenario, but I
was impressed at how each individual was already so firm in their
convictions with a proactive approach, showing real initiative. I
found this encouraging because personally I like it when everyone
pulls their own weight in a group and takes responsibility, not only
when things go right and to plan, but (and maybe perhaps inevitably)
also when things go wrong.
Its our first time doing this and it is a new type of experiment
using novel techniques so things are bound to go wrong along the way
as we progress. In science of course any result isn’t a bad result,
but what is important is that results are significant, meaningful,
and that we work well as a team to satisfactorily complete the
project… whatever way we are expected to achieve that!
Early days, but this is exciting and I can’t wait to get started in
the lab. That’s where the magic happens after all.
References:
1. Anjum, A., Zuber, M., Zia, K.M., Noreen, A., Anjum, M.N. and Tabasum, S., 2016. Microbial production of polyhydroxyalkanoates (PHAs) and its copolymers: a review of recent advancements. International journal of biological macromolecules, 89, pp.161-174.
2. David J. Lea-Smith, Steven J. Biller, Matthew P. Davey, Charles A. R. Cotton, Blanca M. Perez Sepulveda, Alexandra V. Turchyn, David J. Scanlan, Alison G. Smith, Sallie W. Chisholm, and Christopher J. Howe (2015) Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle, PNAS 112 (44) 13591-13596.
3. Jambeck JR, Geyer R, Wilcox C, Siegler TR, Perryman M, Andrady A, Narayan R, Law KL (2015) Plastic waste inputs from land into the ocean. Science 347:768 – 771
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