So, after an extended break, normal service is resuming, although the post today will be slightly off the usual topic of the evolutionary journey.

As I mentioned yesterday, I have been writing my bachelor project, and I thought I would share with you a little of the topic I have written it on.

I could write a post which would keep my good e-friend Argyle Sock very happy, with lots of statistical stuff in it, but, honestly, if I see the terms “not normally distributed” one more time, my head may go pop!

Also, the actual topic is much cooler than the stats (even though they are very cool too of course!).

I would like to introduce to a group of pigments called anthocyanins.  These are the reason for the colour of blueberries, blackberries, some grape species, olives and many other fruits, and purple or red colourings in flowers, like these pansies:

Violet pansies: The purple colour is caused by anthocyanins in the petals. Image from Wikipedia

The amazing bright red colours you see in autumn leaves is also down to anthocyanins.

So..why have I spent this last semester writing about pretty red colours? is where it gets a little more interesting (not that pretty purple flowers are not interesting of course!)

Anthocyanins are also found in leaves which are not about to fall off the tree.  Some plants have red leaves when they are young, and some plants can turn on and off the red colouring under certain conditions

Sciencey term for the day: This is called phenotypic plasticity….a phenotype is the appearance something has due to certain genes being expressed. If a phenotype is plastic, it means it can change under certain environmental conditions.

So, I have been looking at a particular plant, which is usually green and grows in shallow lakes.  These lakes dry out a bit in the summer (Yes, we have summer in Denmark, sometimes!), and so some of these plants may end up out of the water.  If this happens, 90% of these plants turn red, until the water covers them again.

The reason I have been looking at this plant (with a bunch of other people who are much better at scary maths than me!) is because it is not entirely clear exactly what the red stuff in the leaves does.  In some plants it seems to act a bit like a sunscreen, in others it seems to stop the plant being eaten by insects.

The amazingly awesome Leaf-cutter ants (Several posts on them will come along a bit later in our evolution journey) will not harvest leaves which are red. This may be because insects do not see red the way we do, they do not have the parts in their eyes which can collect red light.

Leaf Cutter Ants carrying leaves off to their underground farm Image from wikipedia

It has also been suggested that anthocyanins can help plants survive during cold or drought conditions, so, there seems to be a whole lot of stuff that this pigment helps with.

The health food industry has even been getting in on it, and you can buy anthocyanin supplements…this is because in plants, they work as anti-oxidants, and we are always hearing about how having free radicals is bad for us, and so we should eat blueberries, or whatever the cool food to eat this week is (its usually the most expensive one!).  I am not entirely sold on this idea, as, last time I checked, I am not a plant.

So anyway, I have been working with an awesome group of my fellow students, and we have been trying to make these poor plants very stressed to see what happens. We grew them under some very bright lights, and then did some tests where we zapped them with..well…an even brighter light, to see what they did.

Personally, I find the plant we have been studying more interesting than the actual pigment we have been looking at, although, that has been fascinating to learn about.  The plant itself has no stomata, which are the holes which plants use for taking in carbon dioxide and giving out oxygen and look like this in extreme close-up:

Stomata on a tomato leaf Image from wikipedia

Because this plant has no stomata, it has to breathe through its roots, which is extremely cool!  This means that it can only live in lakes which do not have a lot of nutrients in them, because, if you increase the amount of nutrients which end up at the bottom of a lake, you decrease the amount of carbon dioxide which is produced by the bacteria eating all the dead stuff at the bottom.

As more dead stuff ends up at the bottom of the lake, the bacteria down there start using up more oxygen than is available, and so the only ones that can live there produce methane (CH4) instead of carbon dioxide (CO2). This is what is found in my favourite land-types, the wetlands, bogs and moors.

Oh, yes, I forgot to show you a picture of the plant!  This is the little thing I have spent 6 weeks growing, and then several weeks cutting up and zapping with bright lights!

Lobelia Dortmanna. Image from wikimedia

So, I hope I did not bore you too much with the slightly off-topic post, and next time we will pick up on the evolutionary trail again, with some weird and wonderful creatures. If you prefer plants, hang in there, we will get to them in a few million years or so!


Leaves, keys and fungi

So, there was this story yesterday in the Guardian about how ash trees are at risk from a fungus:

This topic has been in the media a fair bit lately, but very few of the stories have gone into the mechanisms and details, so I thought I would write briefly about those, as they are fascinating, and can help with understanding the problem better.

Most of the stories in the media have just said that it affects leaves, which is a very vague description.

So, first of all, to make sure we all know the tree we are talking about, this is an Ash tree, otherwise known as Fraxinus excelsior:

Fraxinus excelsior, the common Ash. Image from Wikipedia

And here is it’s close-up (It doesnt get red-eye like I do, and is always photogenic!)

Close up of the leaves and “keys” (fruit) of the common Ash. Image from Wikipedia

So, now we have met the victim, lets meet the perpetrator (Sorry, I am catching up on CSI episodes at the moment, so excuse me if I go a bit Horatio Caine).

This is where it can appear a bit confusing, because this fungus actually has two names:  The one most mentioned in the media is Chalara Fraxinea and it looks like this when it is grown in a lab:

Chalara fraxinea, politely posing in a petri dish. Image from Federal Institute of Technology Zurich

This is the fungus mentioned in the Forestry Commission factsheet about this problem (See further reading for link).

This is what is known as an anamorph, which means it is the asexual reproductive phase of this fungus.

I think the reproduction of plants, fungi and small micro-organisms is really cool, so I am going to explain it a bit here as it can seem a bit confusing (I remember getting tied in knots trying to revise this for functional biology!)

The asexual reproduction of fungi such as this species involves producing spores (from the greek spora, which means seeding, or sowing), which you might know from the puffball mushroom, when you kick it, it gives off a load of dust-like stuff, which is actually the spores for the next generation of the fungus, which looks like this:

Puffball mushroom releasing its spores. Image from wikipedia

Each of those spores is a potential new fungus, provided it lands in a suitable environment for growth.  This method of dispersal is very haphazard, and this is why these organisms produce so many spores.  It is a bit like closing your eyes and throwing a handful of seeds randomly out on a bit of ground and hoping for the best.

They are formed by mitosis, which is also how our cells in our body are replaced and is in itself a really really cool process (especially when you see slides of it), and which I will cover in depth in a later post.

As I mentioned earlier in this post, this fungus has two names, the asexual form C.fraxinea and the sexual form Hymenoscyphus pseudoalbidus. Now, maybe it is just me, but I found it a little confusing initially to understand how one organism can have two names, or even two life cycles when I first started reading about this.

This image shows the life cycle of an Ascomycete, which is the group of fungi which this particular one belongs to.  The asexual cycle is the loop off to the left of the diagram.

General life cycle of an ascomycete. Image from Penn State University

From what I gather from reading several journal articles on this species, it seems that the asexual form is on the leaf litter, and dead wood on the forest floor, and this is not infectious (or pathenogenic to use the sciencey word).

It all goes a bit nasty for our Ash trees when it is in the sexual form, H.pseudoalbidus .  It is called “pseudoalbidus” because there is another species called H.albidus which is not responsible for this problem in Ash trees, but appears physically similar.

This is what the fungus looks like:

H.pseudoalbidus on a branch. Image from Institute of Technology, Zurich

This confusion with two different names for the sexual and asexual form of fungi will be less confusing soon, as in 2013 they are changing the naming structure, so that there is one name for a species of fungi, regardless of which stage of the life cycle it is in.

As you can see from the diagram, the asexual form of the fungus only refers to the spores,  everything else within its lifecycle is classified as H.pseudoalbidus. Calling this C.fraxinea in the media is quite confusing, but understandable, as many journals refer to this fungus as C.fraxinea.

The cycle of infection appears to be, that the spores remain in the litter, or on dead branches over the winter, and then, in the summer, it germinates, and becomes the white mushroom thingies.  These release spores, which are spread by the wind, and some end up on the leaves of Ash trees, and on the branches.  These form structures known as mycelium which are basically a mass of threads, and it is these which are responsible for the damage to leaves and branches, if they get into a gap in the bark, they form lesions like on this branch:

Necrotic lesions on a branch. Image from EPPO (European Plant Protection Organisation)

These are also known as cankers, and result from the death of the tissues.

The fungus also damages the leaves, as shown in this image:

Leaf dieback as a result of fungal infection. Image from EOL

The dead branches and leaves then fall to the floor, and the cycle begins again.

This is a relatively new infection in Ash trees, first being noticed in the mid 1990s.

There are ongoing discussions as to why this has arisen, as this fungus has been known since the late 1800s, but as the non-infectious H.albidus.  There is discussion about whether climatic stress has weakened the trees resistance to infection, or whether the infectious version of this fungus is better suited to the milder climate conditions over recent years, or whether this new infectious form is a mutuation which has arisen recently.

Whatever the cause, the result is devastating. Denmark has lost around 90% of its Ash trees since the infection arrived, and other European nations are reporting large scale losses of Ash trees.  The infection appears to have arrived in the UK (Which is usually protected from these types of infection because of its island status) by importing of young trees which were carrying the fungus.

So far, it seems that the fungus has not managed to infect “wild” trees in the UK, and the government has begun a consultation, which will end on the 26th of October, which could lead to a ban on imports of Ash (and given the severity of the threat, I would hope that a ban is imposed).

Further Reading: (Most are very easy to read, with the exception of the journal article at the end, they are mostly from the Forestry Commission, and similar bodies) (Rapid Risk Assessment)$FILE/pest-alert-ash-dieback-2012.pdf

Krautler & Kirisits: The ash dieback pathogen Hymenoscyphus pseudoalbidus is associated with leaf symptoms on Ash species (2012)



Oxygenation of the atmosphere – or why we love bacteria, part I

One of the critical steps in the development of life as we know it today was the evolution of cyanobacteria (also called blue-green algae).  These single-celled organisms are responsible for adding oxygen to the atmosphere, and paving the way for the higher life forms that we have today.

They were not the first autotrophs (organisms that generate their food directly from sunlight, or inorganic chemicals, as opposed to heterotrophs (like us), who get their carbohydrates second-hand by consuming other organisms),  one view is that organisms similar to purple sulfur bacteria existed first, and it is the transition from these to cyanobacteria that today’s post is about.

Purple sulfur bacteria are only able to grow under anaerobic conditions (that is, conditions without oxygen present), because the synthesis of pigments in the cell is suppressed if oxygen is present. The early atmosphere of the earth was not oxygenated as it is today (as evidenced by sulfur isotopes in rocks over 2.45 billion years old, among other indicators), although there is some debate about the exact timing of the first atmospheric oxygen (NB: This does not mean I am saying “Science does not know what happened”….the time period in discussion is a few million years, and the discussions are about whether any atmospheric oxygen was immediately reacted with iron or other chemicals in the oceans).

Ok, so about these cute little purple sulfur bacteria, they are photosynthetic, so this means they use sunlight to obtain their carbohydrates.  Unlike plants today which use chlorophyll (the reason they have a green colour, but more on that later), these purple bacteria use a compound called bacteriochlorophyll, which uses different wavelengths of light, and does not produce oxygen as a waste product – This is kind of handy, since, as we saw in the previous paragraph, sulfur bacteria do not function so well in the presence of oxygen.

So, I have just mentioned photosynthesis, which is the method that plants use to obtain sugars from sunlight.  The equation for this in sulfur bacteria is as follows (Simplified version).

CO2 + 2H2S → CH2O + H2O + 2S, (or carbon dioxide + 2 lots of hydrogen sulfide is converted using light to carbohydrate + water + 2 sulfur molecules.)

Hydrogen sulfide is the rotten egg smell, and is emitted by volcanos.  The early earth was very geologically active, and volcanic activity was much higher than it is today, providing plenty of hydrogen sulfur for these bacteria to use.

This equation is important, because it was the discovery of this method of photosynthesis which demonstrated that it is water, and not carbon dioxide which is used for producing oxygen.  Prior to that, it was thought that the carbon dioxide was split to produce the waste product of oxygen.

So, back on the early earth, there were these bacteria pumping out sulfur, and using up the CO2 and H2S from volcanos.  Because they were purple, they used light in a different wavelength to the  plants of today, which reflect back the green portion of the incoming light, and thus we see them as various shades of green.  These purple sulfur bacteria reflected light back at both the higher end of the spectrum (red) and the lower end (blue), giving them their colour.

Absorption of light for purple and green chlorophyll pigments.

(Image from )

So, now we have oceans filled with reddish purple bacteria! I always try imagining how our planet would have looked back then, not so much a pale blue dot with green patches, but more likely a vivid colour like we see today when we get blooms of purple sulfur bacteria in places like Yellowstone park and other oxygen low, sulfur rich hot springs.

The next development was for some bacteria to evolve to use the light that was not being used by these organisms.

As you can see from the image, the purple bacteria would have used the light at in the centre of the spectrum, leaving light at the ends available for use, so any organisms which evolved to utilise this would have had a competitive advantage. If you want to know more about the evolution of cyanobacteria, without getting overly heavy on technical stuff, there are two systems within plants which do the conversion of light, these are called Photosystem I and Photosystem II. Green sulfur bacteria have Photosystem I only, and purple bacteria have Photosystem II only, so it is currently thought that the evolution of an organism which had both, either by endosymbiosis, or by sexual reproduction (yes, bacteria get it on too!) led to the cyanobacteria. (This is not my main area of interest, so please feel free to correct me if I got that wrong).

Ok, so now we have bacteria that reflect light in the green region, and use it from the ends of the spectrum, and have two photosystems…so what?

Well, it so happens that chlorophyll (the pigment involved), when using electrons to generate energy, gets electrons by splitting water, instead of hydrogen sulfide.  (This happens in photosystem II, in case you were wondering) So, now we have a new equation for photosynthesis, which is more familiar:

CO2 + 2H2O → CH2O + H2O + O2

By using water (which was in abundance), and producing oxygen (which the sulfur bacteria could not tolerate), the cyanobacteria gained a large evolutionary advantage.  In addition, due to the release of oxygen into the atmosphere, ozone was formed by the reaction of sunlight with oxygen to form O3

Ozone is what is primarily responsible for filtering out the UV from the sun, so once atmospheric oxygen, and ozone were in place, the stage was set for the long evolutionary road which would eventually lead to me sitting here typing, and you sitting somewhere else in the world reading these words.