When is a fungus not a fungus? When its an oomycete…

If I asked you to name a microbe that can cause disease in plants you are likely to name a species of bacteria, fungus or virus. But would you name an oomycete?

An A. thaliana leaf infected with downy mildew. The oomycete H. arabidopsidis is shown in blue. Image by Caillaud et al. (2014) licenced under CC-BY.

An A. thaliana leaf infected with downy mildew. The oomycete H. arabidopsidis is shown in blue. Image by Caillaud et al. (2014) licenced under CC-BY.

At first glance oomycetes look quite like fungi because they grow by producing branching filaments—similar to fungal mycelia—through which they absorb nutrients from their surroundings. Oomycetes used to be classified as fungi but, in fact, they are not closely related.

The cell wall that surrounds oomycete cells provides a clue of where they fit in the tree of life: it is made of cellulose, not chitin like fungi, suggesting that oomycetes are more closely-related to algae or plants. This is supported by other features of the lifestyle of oomcyetes and analyses of their genetic information, which place them in the same Phylum as brown algae and diatoms (1).

Oomycetes are responsible for causing many diseases in crop plants, including late potato blight and downy mildew in grape. A severe outbreak of late potato blight in the 1840s led to the Irish Potato Famine, which killed a million people and forced many others to leave the country. Despite this, the oomycete that causes late potato blight—Phytophera infestans—is still sometimes called a fungus.

Understanding how oomycetes infect plants could help us to develop disease-resistant crop varieties to help control these diseases. A recent paper published in PLOS Pathogens studied the relationship between an oomycete called Hyaloperonospora arabidopsidis and its host, the model plant Arabidopsis thaliana (2).

H. arabidopsidis infects A. thaliana leaves producing yellow and brown patches to appear on the leaves, known as downy mildew. To get nutrients from its host, the oomycete produces a special structure called a haustoria that invades into plant cells. The haustoria is separated from the plant cell cytoplasm by a membrane that joins the plant cell membrane. The plant launches several defences to fend off the oomycete and the haustoria gradually becomes encased by a polymer called callose, but it is not clear how this works.

Caillaud et al. found that a plant protein called PDLP1 is found in the membrane surrounding haustoria and is involved in plant defence against the oomycete (2). The experiments suggest that its role in plant defence is to promote the deposition of callose around the haustoria.

PDLP1 belongs to a family of proteins that are found around the channels “or bridges” that connect neighboring plant cells, known as plasmodesmata. Plasmodesmata allow proteins and other molecules to move between plant cells, but sometimes this is not desirable and so the plasmodesmata can be closed to isolate individual cells. To close a plasmodema, the PDLP proteins promote callose deposition around it. Therefore, the experiments suggest that callose deposition around haustoria and plasmodesmata may happen in a similar way and involve the same proteins.


1. Wikipedia: oomycete (retrieved 25/11/14)

2. Caillaud, M., Wirthmueller, L. et al. (2014) The Plasmodesmal Protein PDLP1 Localises to Haustoria- Associated Membranes during Downy Mildew Infection and Regulates Callose Deposition. PLOS Pathogens.

Book review: Cells to Civilizations by Enrico Coen

cells to civilisationsIn Cells to Civilizations: The Principles of Change that Shape Life, Coen presents evolution, development, learning and culture as transformational processes that share seven fundamental principles. To start with it felt strange to read about familiar concepts in terms of Coen’s seven principles, but I liked how it made me think about the processes in a different way. I enjoyed Coen’s explanations of his processes and the diagrams were clear and very useful. However, while it was clear why it can be useful to think about evolution, development and learning using a set of shared principles, I wasn’t quite so convinced of the relevance of thinking about cultural transformations in the same terms as the biological processes. With famous works of art featuring in many of Coen’s explanations throughout the book, the book is an unusual, but quite interesting mix of science, philosophy and art.

All in all, I enjoyed reading this book and would recommend it to anyone with an interest in evolution, development and learning. To get the most out of the diagrams in the book I would suggest reading a print copy as I found referring to diagrams on my kindle a bit cumbersome. For a more in depth review follow this link.

Industry: old friend of woodlands

Ancient woodland in Ashridge Park, managed by the National Trust. Image by UKGardenPhotos via flickr (CC BY-NC-ND 2.0)

Ancient woodland in Ashridge Park, managed by the National Trust. Image by UKGardenPhotos via flickr (CC BY-NC-ND 2.0)

Like many of the environments we call “natural”, woodlands in the UK and Europe have actually been shaped and changed by humans. Most have been carefully managed for centuries to produce wood, a valuable resource with many uses. In many regions, woodland has been relatively scarce for a long time, and woods tended to be owned either by individuals or the communities that maintained them.

The predominant form of woodland management was coppicing — a low-impact practice dating back to 4500 BC (1), where trees are cut down to the base and left to regrow new shoots before cutting again (see my recent blog post). The thin coppice poles produced would have been a handy shape for a variety of uses including fencing, charcoal production, firewood and furniture. To produce larger diameter wood or ‘timber’ for buildings or shipbuilding, some of the trees in a coppice – known as standard trees — were left uncut for longer periods before felling. Coppicing remained most common form of woodland management until the 19th Century, when the increasing demand for timber led to a new fashion for plantations (2).

Charcoal was traditionally made from heating wood in the absence of oxygen. Image by  Ischaramoochie (CC BY-SA3.0)

Charcoal, which was traditionally made from coppice wood was used for fuel in many industries. To make charcoal, wood is heated in the absence of oxygen. Image by Ischaramoochie (CC BY-SA3.0)

It is commonly believed that industry is bad for woodlands, but over the last 2000 years, the most common reason to clear woodland in the UK was to make way for agricultural land.. The industries of the time relied heavily on wood for fuel and other uses, so more industrial areas — such as the Methyr Valley – tended to keep more woodland than agricultural areas like East Anglia (3). Unfortunately, by the mid-19th Century coal and coke were replacing wood and charcoal as fuel for many industries and so the demand for coppiced wood dropped.

 The 20th century was pretty catastrophic for UK woodlands. By this time the UK imported 90% of its wood, but this was not possible during the First World War (1914-1918). To meet the shortfall, 180,000 hectares of woodland was felled in four years (4). The woodlands could have recovered, but unfortunately the newly established Forestry Commission prevented this by setting up conifer plantations on old woodland and scrubland sites. By the outbreak of the Second World War in 1939, they had 230 forests on 265,000 hectares of land (4), but most of the trees were too young to be felled for timber and more ancient woodland was felled.

The UK the government’s agricultural polices between 1945 and 1975 were also very damaging to woodlands. They wanted to increase food production and grants were provided to clear woodlands and hedgerows, leading to the destruction of nearly half of the remaining ancient woodlands in the UK. Most of the extra land was unnecessary because significant increases in crop yields were being generated through crop breeding and use of chemical agents including fertilizers and pesticides (1).

A turning point for UK woodlands came at the 1992 Rio Earth Summit, where the UK government pledged to conserve and expand semi-natural woodlands (4). The Forestry Commission now started to actively promote their conservation and restoration, including the return to native species and traditional management practices.

Although I have focussed on UK woodlands here, similar trends in management can be seen all over the world. Where wood is highly valued, for example in Canada and Sweden, woodlands and forests tend to be carefully managed. It is areas where wood is plentiful and/or not valued, such as the tropical rainforests, where the fastest destruction is taking place, often to make space for agriculture or mineral mining.

As we try to protect and conserve the World’s woodlands and rainforests, it is worth considering if, and how sustainable industries might be able to help. In the UK, the popularity of wood burning stoves and rising wood prices could make coppicing ancient woodlands a commercially viable option again in future. If the past is anything to go by, demand for wood and other products may help to preserve the World’s woodlands and rainforests better than we can hope to achieve with conservation efforts alone.

Aerial view of the Amazon Rainforest, near Manaus, Brazil. Image credit: Neil Palmer (CIAT). (CC BY-SA 2.0)

Could sustainable industries help to save the Amazon rainforest? Aerial view of the Amazon Rainforest, near Manaus, Brazil. Image credit: Neil Palmer (CIAT). (CC BY-SA 2.0)

This article is the second in a series entitled Focus on… Woodlands:past, present and future. In the first post I discussed the use of coppicing, a traditional woodland management practise. Future posts will feature a case study about my favourite local ancient woodland (Lower Wood) and the future of coppicing.


1) Rackham, O., (1990) Trees and Woodland in the British Landscape, J M Dent

2) Rackham, O., (2010) Woodlands, Collins

3) Rackham, O. (2003) Ancient Woodland. Its History, Vegetation and Uses in England, Arnold

4) Agate, E., (2005) Woodlands a Practical Handbook, BTCV

Book review: The Simpsons and their Mathematical Secrets by Simon Singh

Image by Richard Cooper (CC BY-NC 2.0)

Image by Richard Cooper (CC BY-NC 2.0)

The Simpsons and their Mathematical Secrets is a light-hearted look at the mathematics hidden in the popular animated TV shows The Simpsons and Futurama. The author Simon Singh — a big fan, and best selling author of books including Fermat’s Last Theorem  — highlights some of the many mathematical story lines and jokes that appear in the shows, taking care to explain the concepts for a general audience. The surprisingly large volume of mathematics in both shows is due to the mathematical backgrounds of many of the writers involved, many of whom worked in academia before joining the shows. For me, the book was a fun reminder of mathematics I had previously learnt and an introduction to other concepts I had not come across before. I really enjoyed reading this book and would highly recommend it to anyone who enjoys watching the shows. For an in depth review follow this link.

Check out reviews for other books I have read recently on my book reviews page.

The “perfect” commute

Train arriving at Wymondham station, Norfolk. Image by Steven Hughes (licenced under CC BY-NC-ND 2.0)

Train arriving at Wymondham station, Norfolk. Image by Steven Hughes (licenced under CC BY-NC-ND 2.0)

For my new job I travel to Cambridge, which is 60 miles away from where I live in Norwich. It takes me about 1 hr 40 minutes each way, with most of that time spent on the train. Since commuting now takes up a significant chunk of my day I have been thinking about how it is going so far, and if there is anything I can do that might make it better.

Instead of just making a list of the good and bad aspects of my commute I decided it would be more fun to compare it to my vision of a “perfect” commute.

The “perfect” commute is:

Always shorter than your own. I think there are very few people who are entirely happy with the length of their commute. Even use of the word “commute” tends to imply that the journey to work is quite long. I didn’t consider my 15-20 minute journey car journey to my old job as a commute… Continue reading

West African tulip: a living water pistol

Drawing of West African Tulip (Spathodea campanulata).  Drawing by L. A. L. Constans - Paxton's Flower Garden, volume 3, (public domain)

Drawing of West African Tulip (Spathodea campanulata). Drawing by L. A. L. Constans – Paxton’s Flower Garden, volume 3, (public domain)

I recently visited The Gambia in West Africa. The purpose of my trip was to work on a GirlGuiding community project, but I did manage to spot some interesting plants along the way. The Organism of November is a tree I saw a lot around the urban area — near the capital Banjul –where I stayed.  It is known as the West African tulip tree and produces beautiful bright orange flowers all year round.

Also known by its latin name, Spathodea campanulata, the tree is a member of the bignonia family (Bigonaeceae). It was “discovered” in 1787 in the Gold Coast and is native to much of West Africa including The Gambia. It can grow to 50 feet or more in height. Continue reading

Guest post. Jack O’lanterns: Pumpkins and turnips and fungi, Oh My!

Pumpkin harvest in Poland. Image modifed from original image by titidianita [CC0] via Wikimedia Commons.

Pumpkin harvest in Poland. Image modifed from original image by titidianita [CC0] via Wikimedia Commons.

By Kirsty Jackson (@kjjscience)

Legend has it that at this time of year the bridge between the living and the spirit world is at its smallest; and on Halloween spirits and fairies are able to cross over and spend the night walking in the land of the living. But don’t panic this has never been scientifically proven and a good Jack O’lantern will keep you safe.

A Jack O'lantern carved from a turnip. Image by Geni [image availble under a CC-BY-SA-3.0 licence] obtained from Wikimedia Commons.

A Jack O’lantern carved from a turnip. Image by Geni [image availble under a CC-BY-SA-3.0 licence] obtained from Wikimedia Commons.

In Ireland people traditionally carved from turnips (sweed if you are from the south of the UK) or large potatoes to frighten away the spirit of Stingy Jack. The story goes that after repeatedly tricking the Devil, Stingy Jack was not allowed into heaven or hell but was given some burning coal which he put into a carved turnip to light his way as he roamed the earth for all eternity. The tradition of lantern carving was taken over to America with the Irish settlers. Pumpkins, native to North America, turned out to much easier to carve than turnips and make ideal lanterns. This week children and adults all over America will be carving pumpkins into Jack O’lanterns to mark the holiday. Now in the UK pumpkin carving has risen in popularity and is overtaking the traditional turnip carving. Continue reading