Blog Archive

Wednesday, 27 April 2016

Bacteria can Chill Out too!

I'm excited, I just found a new use of friendly bacteria I didn't know about!

Pseudomonas syringae is a pretty nasty plant pathogen. In fact, a lot of my reading for my project involves inhibiting or otherwise deterring it from infecting plants. But even a common disease causer like this can have its uses!

Because bacteria are so tiny, they can interact with things much smaller than we can. For example; water! Clouds are full of bacteria (see this blog post for more details) condensing water vapour together, but that's not all they can do. P. syringae can freeze water! Only a few degrees above normal freezing point, but a few degrees can make a huge difference (just look at the climate change stats!). This cool paper shows how they do it; they use proteins to move the water into structured arrangements which encourages freezing.

Why does this make them 'friendly' though? Well, they're used extensively in making artificial snow slopes! I had no idea about this, it's pretty awesome.

It's not just Pseudomonas that can make snowmen!

On the less friendly side of things, it also is bad news for plants; not only does P. syringae cause disease but it increases the likelihood of frost damage too. Which just goes to show; while bacteria may cause adverse affects in certain conditions, in others they can be really handy!

Saturday, 23 April 2016

E. coli: the 'E' isn't for 'Evil'

It actually stands for 'escherichia' (which doesn't exactly roll off the tongue, hence always just being called E coli).

Yesterday I was reading something about superbugs, and it listed E coli as one of the deadly ones. Everyone's always on the lookout for E coli contamination in food, restaurants, bathrooms etc. But is it really as scary as it's portrayed in the media?

Some strains are, definitely. K2 causes meningitis in newborn babies, O104H4 causes pretty nasty kidney damage (an outbreak in 2011 killed 52 people across the world) and scarily-named 'Entero-haemorrhagic E coli' strains like O157 cause bloody diarrhoea. Obviously being infected by any of these are on nobody's to-do-list, but just as the majority of bacteria as a whole don't cause disease, there are a huge range of E coli strains that aren't a threat at all. In fact, pretty much everyone has E coli as part of their normal community of gut bacteria! Animals included. That's partly why it's always looked for in restaurants and stuff; if it's in the intestines, then it'll be in what exits the intestines... so when they say 'we found E coli in 4/5 restaurants' they're basically saying there's faeces all over the place, so you should probably eat somewhere else until they start washing their hands! E coli  is therefore the poster boy for faecal contamination, but it's often more of a sign of contamination rather than the worst bacteria in there. It's just that it's much easier to  grow in the lab to detect, and that nowadays when there's so much genetic screening it's again easy to look for as we've got the whole genome sequenced. Often, food poisoning bacteria like Campylobacter jejuni are much more picky about what they want to grow on in the lab so it's quicker, cheaper and easier to just look for the E coli.

This is where E coli starts to redeem itself though; because it's so happy in lab conditions, it's really easy to work with! Everybody should love E coli. Not only is it easy to grow, it's pretty easy to insert genes into via various methods so we can customise it to be useful for all sorts of applications. One of the first examples of this, and one of my favourite examples of Friendly Bacteria, is the E coli that have been modified to produce human insulin. They first did this back in the seventies, and insulin is still made in this way to this day! Yeast is used sometimes too. Before that, they had to cut it out of corpses, or from pigs (which needed lots of accompanying medication).

I couldn't list all the ways E coli is used; a quick search for it on Google Scholar gives more than two and a half million different research papers using it! It's fair to say that without E coli we'd all be a lot worse off.

So should we fear E coli? No! It's our friend! (Apart from the baby-meningitis/bloody diarrhoea ones, feel free to fear them as much as you like)

Thursday, 21 April 2016

Chilling on the beach; Student life Aber style

I went down to the beach yesterday evening, had fish and chips and just sat there with friends until after sunset. For me, this sums up all the best parts of being at University here in Aberystwyth; good friends, beautiful scenery, and a hugely relaxed yet fun atmosphere! Here's a bunch of photos I took:

The last one's looking out the window through some scaffolding that's up at the moment, but it was too good a view to not capture!

Wednesday, 20 April 2016

Vlogging; Scientists Are People Too

Weekly Vlog #2! I thought I'd combine this week's vlog with today's blog post to just say why I'm doing it and things like that.

So why am I doing a vlog? I'm ridiculously, painfully shy when talking to anyone. The thought of being the centre of anyone's attention fills me with dread! So why talk about my everyday life and put it out there for the world to see?

Firstly, precisely because it's really scary to me. I both want and need to be better at communicating, not only for things like conferences or my Viva but for general life too. I can barely bring myself to answer the phone, and things like social events or whatever cause me to retreat behind my walls and clam up like... well, a clam. This isn't good, and really holds me back socially which has knock-on affects throughout my life.

Secondly, I want to show that scientists (I know I'm just a PhD student but I'm calling myself one anyway) are people too! Everyone thinks of them as these scary figures in labcoats and rubber gloves but really it's just another job; scientists have fun, go to the pub, go on days out, just like any other person. I want to try and get that message across, and make science seem more accessible and enjoyable; really, anyone can participate in science in one way or another, and everyone can enjoy it!

So that's why I'm doing it. Feel free to tell me how I'm doing, good or bad!

Friday, 15 April 2016

Handy Bacteria

No, not bacteria that can put up your shelves or fix the sink, or even ones that are useful to us... I'm talking hand bacteria! On your hands!

I mentioned before how pretty much everything is harbouring all sorts of bacteria. That definitely includes our hands! Skin is covered with salts and oils and stuff like that that bacteria find super tasty, and that's just average skin! We constantly touch things with our hands, getting tiny but significant amounts of all sorts of stuff (including more bacteria) on them. Now, don't be scared by the whole 'completely coated head to toe in bacteria' thing because as I've said before the overwhelming majority of them won't hurt us! But depending on what you're sticking your hands on, you might pick up something grisly like salmonella or whatever. That's not just touching chicken, though; if Edgar touches a contaminated chicken fillet, then touches the taps or door handle, there'll be salmonella on there, which can get on your hands even if you don't go anywhere near the chicken! Also, never ever wash raw chicken unless you like the idea of spraying tiny droplets of food poisoning onto every surface of your kitchen...

Anyway this isn't a post about food safety, it's about the hand bugs! Recently some researchers found that by comparing the bacteria on your hands to the ones on your belongings, like your phone or keyboard, they can actually get a pretty decent picture of who owns which thing! They'd like to use it for forensic stuff but that's a long way away if it ever happens at all.

Hooray! You thought I was going to be talking about food poisoning and telling you to wash your hands, but no! I pulled it back to the friendly bacteria again, this time crime-solving bacteria! Is there anything they can't do?!

We just watched Bone Tomohawk, it was great but the amount of wound infections and stuff they were constantly risking seemed crazy! We really take for granted how much we know about not getting gangrene that folks back then had no idea about... I guess we take 'not getting killed with an axe' for granted too but I'm here for the microbes not the axe murders!

Good film though, check it out!

Wednesday, 13 April 2016

They Came From Above!

Bacteria are everywhere. In your mouth, in your bed, at the bottom of the sea, underground, anywhere you can name that isn't really hot, really acidic or otherwise too hostile for life. But how did they get there? Some animals are found all over the place but they have stuff like wings and legs and Double Decker buses, bacteria don't have any of that!

On a small scale, they can kind of swim along with big floppy oars/propellers called flagellae, but I'm thinking bigger than that. Of course in the sea they can just float around on the current hoping they don't get eaten by whales, but on land? How did they get to Australia? Or Hawaii?

The key to this is partly their numbers. Being microscopic is less of a problem when there's billions of you, so while individual cells won't make the trip up a mountain or even across the floor the colony as a whole might spread there just by multiplying. Plus, due to their impressive rate of reproduction, even single cells getting to a new place can lead to it being colonised. Bacteria on migrating birds for example can be transferred to new lands. But one of my favourite routes of global bacterial transmission is via the clouds!

Clouds are full of bacteria. In fact, it's been shown that above about four degrees Celsius dust particles can't gather water vapour to form cloud particles, and bacteria are much more likely culprits. Just like marine bacteria float on ocean currents, airborne cloud bacteria can be carried all over the world! 

I used to work in a lab looking for thermophilic bacteria in soil samples from the UK. These bugs were needing temperatures of sixty to seventy degrees, so why were they in cold British soil? There's a weather phenomenon in Britain and Europe where everything gets covered in sand blown up from the Sahara desert, and the same winds can carry thermophiles to distant lands! I was working with Geobacillus, which can hibernate in spores for a huge amount of time, so they just kept getting added to the soil by the wind and rain. They were just sitting there for me to find!

Don't worry too much though: any bacteria in the rain are in too small numbers to cause you any harm. After all, most bacteria are friendly!

Sunday, 10 April 2016

Saturday, 9 April 2016

Friendly fungi: trip to the Penderyn distillery (and brewery)

I'm late posting this (and it'll be short) as I've been out today: we took my dad to a whisky distillery as another birthday treat! They had a brewery on site so the microbiologist in me was excited!

Breweries use yeast (saccharomyces cerevisiae) to create the alcohol. They do this by feeding them a sugar source, in this case barley grist, and taking away all the oxygen. This makes the yeast stop using the oxygen for respiration so in order to still get energy it ferments the sugars to ethanol, which gives the drinks their alcohol levels. Ethanol does eventually kill the yeast if there's too much of it, which is why you can't get much higher than fifteen or so percent without distilling it!
We saw that process too, with the big fractionation columns, then got to try some of the end product (and even some of the raw 92% stuff!) Which was delicious!
It was a fantastic day, and for me was great to see some friendly microbes being put to good use! Thanks, Penderyn!

Wednesday, 6 April 2016

Taking care of your new pet bacteria

Bacteria have a lot in common with the bigger organisms we all know and love. They need energy, warmth, and all sorts of nutrients in order to grow and live happily. By the way, when talking about bacteria 'grow' normally means 'divide by mitosis to form two daughter bacteria' rather than getting bigger. The great thing about bacteria is, they have adapted to be able to use a huge range of sources of energy and nutrients! Some, like cyanobacteria, harness the power of the sun like plants do. Others live so far underwater that there is no light, so use heat and sulphur and things from deep-sea thermal vents like white-smokers. For food, there are bacteria that can eat pretty much anything; if anything says 'biodegradable', that's just another way of saying 'bacteria can eat me!'

So how do we accommodate these weird and wonderful needs in order to take the bacteria from where they've evolved to live to a much more convenient (for me) laboratory? To be honest for a lot of bacteria we still don't know the answer; only a small proportion are able to be 'cultured', or grown in the lab. We can still find out about the picky ones by sequencing their DNA though, don't worry!

The ones we can grow in the lab do need a bit of looking after. It's a bit like looking after a pet Rabbit! First, you find an enclosure for them; rabbits have hutches, bacteria get petri dishes. Next, they'll need some 'bedding'. Rabbits get hay, which they also like to eat, so in the same way we give the bacteria an agar gel containing nutrients. This gives them a place to grow, and also the food they need! There are a lot of different rabbits but they can mostly be kept fed with the same mix of rabbit food, and once again bacteria are the same. They need a source of carbon, like sugar, some nitrogen, like in ammonia (although some can use it straight from the air), phosphates, and salts. (Of course it's a bit more complicated than that but that's the quick version!) These are all in 'general media' like the well-named 'nutrient agar'. This can then be modified to cater for a particular bacteria or family of bacteria. Some bacteria need to be grown in agar containing blood! Other common things are things like yeast extract, iron or sulphur.

They even look similar! You see it too, right?

Now that they've been fed and housed, we need to work out where to put the rabbit/bacteria. If you put the rabbit hutch in deep shade all winter, you might have some poor frozen bunnies inside. If you put it in full sun over the summer months, they'll start to cook! Bacteria are very similar. Some are happy at room temperature, some need 37 degrees celsius (our body temperature... this is ideal for human pathogens, so I tend to avoid it in my experiments) and some 'thermophiles' like Geobacillus need temperatures around 60 to 80 degrees! I think the highest growth temperature recorded is around 118 degrees (which is crazy! They can survive being boiled!) in some extremophilic bacteria. And archaea too, which is another microbe kingdom like bacteria and fungi. This is pretty easy to control these days though, there are all manner of fancy incubators that can go up to any temperature your pet rabbit bacteria enjoy!

Some don't mind a bit of heat!

That's pretty much it, to be honest. Different bacteria need different things so it's impossible to describe everything in a short blog post but I did my best! Maybe someday soon we'll be seeing bacteria in a cage at the pet shop... There is a microbe zoo in Amsterdam so it's only a matter of time!

Saturday, 2 April 2016

So who am I then?

I've been doing this blog for a little while now, but haven't really gone into much detail about myself. So who am I? Why do I like friendly bacteria so much? And why am I doing this blog at all?

I'm a twenty three year old PhD student with a microbiology background, in the first year of my PhD. I'm working with a type of friendly bacteria called endophytes, which live in plants and can help them grow and resist disease in exchange for a safe, stable place to live. It's fascinating! It's a bit like the bacteria in your intestines, they don't hurt the plant at all and can even provide good things like hormones and nutrients! I've got a long way to go before I finish but I'm loving it so far so I'm sure it'll fly by.

So why do I like friendly bacteria? Since a young age I've been amazed by the power bacteria have. These tiny creatures so small you can't see them can have huge effects on people, and even the whole world. Just look at the old plagues! The black death killed a huge proportion of the population of the world, but the bacteria behind it (Yersinia pestis) is still much smaller than even one cell of a human. Obviously more than one cell of it was involved, but just as a billion harmless droplets of water can cause flooding and devastation, the huge number of bacteria cause illness and death on a huge scale.
This power the bacteria hold captured my imagination. What if we could use that potential for the benefit of mankind? To continue the water analogy, hydroelectric dams use the power of the water for good, and I wanted to do the same with bacteria. This was before probiotics were popular, and I didn't really know about common uses of microbes like brewing or antibiotic production, but I kept that interest alive as I went on in life, and ended up studying microbiology at degree level. I've done some work in an industrial lab looking at bio ethanol production for fuel, and now I'm here working on my plants!
I realise "using microorganisms to improve higher organisms" sounds very Resident Evil (and I must admit that did help keep my interest in it going) but it's very safe and there's no danger of zombies! Although if it did happen nobody would be worried because I'm in the middle of nowhere and there'd be nobody to bite!

That's who I am, and why I'm doing what I do, but why did I start this blog? I'm really keen to get more science widely known, especially about the 'good bugs' in the world. I feel like a lot of people aren't really told much about bacteria, and microbes in general, so tend to throw up barriers whenever they come up rather than finding out about them. All science affects everybody, so I think having an understanding of how things work would benefit absolutely everyone no matter what they do or where they live worldwide. I already tell my family and friends about awesome, interesting things I find out but I want to spread that around and tell the world!
Whether you're a scientist yourself, or a child in school, or work in retail, an office, in construction, wherever, I want to make awesome scientific developments available, accessible and understandable to everybody!