Tuesday, December 18, 2007

Blog break

Since I'm currently located in a country in a warm climate, with lots of good entertainment, food and alcohol, and sadly, less than perfect internet connections, I am forced to take a break from blogging. I should return the first week of January, provided I sober up enough to post something remotely legible. Have a great start of 2008!

Monday, December 10, 2007

Plant Pathology: Gene-for-gene theory

Here is finally the post I promised that I had wanted to write for quite a while, and can finally write because it was one of the questions on my PhD qualifying exams.

In the 1940s, Harold H. Flor, made a large number of crosses of flax rust races (this is not a trivial exercise, you try mating these minute fungi with each other). He then identified how pathogenicity (the ability to cause disease) on flax was inherited (1). He would use all the flax rust progeny he obtained to infect (inoculate) a large number of available flax lines, and he would score the reaction of the plant to the pathogen (immune, resistance, semi-resistant, susceptible).

If that wasn't enough, Flor also made a large number of crosses of the host, each of which was resistant to none, one, or several races of the flax rust pathogen Melampsori lini. So, he would cross two races of flax, cross the resulting progeny with itself, and analyze the second generation. The reason for this is that the genes involved are often dominant and that you do not see the effect of individual alleles in the first generation (if that doesn't make sense, leave me a note in the comments, I'd be happy to elaborate). In the second generation, the recessive genes segregate and you can see all sorts of fun stuff going on. Flor inoculated all the second generation flax progeny to study the inheritance of resistance. He published those results in a separate paper (2).

Flor found that both resistance in plants as well as avirulence (= lack of virulence/pathogenicity; does not cause disease) in the pathogens were inherited. He also noted that even if the plant had a resistance gene (R), it was only resistant if the pathogen infecting the plant had a particular gene, which is now called an avirulence (Avr) gene. That's kind of weird, isn't it? If the plant has a resistance gene, why should it not be resistant to the pathogen all the time?? Flor also found that in almost all the cases he looked at, resistance was dominant over susceptible, and avirulent was dominant over virulent. Note: Flor used the word "factor" instead of "genes."

Based on Flor's results he formulated what is now called the gene-for-gene hypothesis (3):
For every gene in the plant that confers resistance, there is a corresponding gene in the pathogen that confers avirulence.

Since the genetics of both the host and the pathogen need to be taken into account, we pathologists put this in a quadratic check like this:

On the top row are the possible genotypes of the host. Flax is a diploid organism, i.e. it has two copies of every chromosome. As a result, there are two alleles of every gene (one from each chromosome), so the host can be RR (homozygous resistant), rr (homozygous lacking resistance), or Rr (heterozygous, one allele confers resistance, the other does not). Because resistance is dominant, the Rr plant will be resistant and react no different than the RR plants. The same argument goes for the genotype of the pathogen which is given in the first column of the quadratic check, with AA (homozygous avirulent), aa (homozygous virulent), and Aa (heterozygous, one allele confers avirulence, the other does not; the pathogen will act completely avirulent, because A is dominant over a) possibilities. The only way the plant is resistant is if it carries an R gene, and is infected with a pathogen that carries an Avr gene. In all other combinations, the plant will get disease.

From an evolutionary point of view this makes little sense. Microbes propagate very rapidly compared to the host. Why would a pathogen hang on to a gene that will prevent it from making a set of host plants sick? Why why why?? Microbes evolve so fast, you would think that pathogens with mutations of the Avr gene would have a distinct advantage over those that have a functional Avr gene.

The answer to this question is that Avr genes serve some other purpose in the pathogen, or are actually genes that contribute to pathogenicity, except of course, when it is recognized by the host. The exact same gene can therefore be a pathogenicity in one host-pathogen interaction, and an avirulence gene in another. An example of this is Avr4, an avirulence protein from the plant-pathogenic fungus Cladosporium fulvum. The pathogen is avirulent (cannot cause disease) if it has the Avr4 gene, and if the host it is trying to infect (in this case tomato) has the Cf-4 resistance gene. A recent paper (4) showed that if the Avr4 gene is deleted, the pathogen becomes less virulent, and that introduction of this gene in plants, made the plant more susceptible to a number of other pathogens. Avr4 therefore only contributes to resistance if the host has the corresponding resistance gene, Cf-4, otherwise Avr4 is a virulence factor.

The evolution of R and Avr genes is the result of an arms race going on between host and pathogen, where the host tries to prevent the infection, while the pathogen tries to bypass the host defenses to make the host sick (5,6). This can result in evolution at a pace higher than you would expect without this constant battle.

More on avirulence genes in my next mega-post. Which shouldn't take too long to appear, I have a rough skeleton already. In yet another post I will give some examples from Flor's original papers, and explain how he deduced the genetics of the host and the pathogen. The number of crosses he did is mind-boggling.

(1) Flor, H.H. (1946) Genetics of pathogenicity in Melampsora lini. Journal of Agricultural Research 73: 335-357.
(2) Flor, H.H. (1947) Inheritance of reaction to rust in flax. Journal of Agricultural Research 74:241-262.
(3) Flor, H.H. (1955) Host-parasite interaction in flax rust - its genetics and other implications. Phytopathology 45:680-685.
(4) van Esse, H. P., Bolton, M.D., Stergiopoulos, I., de Wit, P.J.G.M, and Thomma, B.P.H.J. (2007) The chitin-binding Cladosporium fulvum effector protein Avr4 is a virulence factor. Molecular Plant-Microbe Interactions 20:1092-1101.
(5) Maor, R, and Shirasu, K. (2005) The arms race continues: battle strategies between plants and fungal pathogens. Current Opinion in Microbiology 8:399-404.
(6) van der Does, H.C. and Rep, M. (2007) Virulence genes and the evolution of host specificity in plant-pathogenic fungi. Molecular Plant-Microbe Interactions 20:1175-1182.

My gift

Last week I got my gift from Sciencewoman in the mail. Thank you Sciencewoman. I really enjoy reading blog, you're a true superhero. And then to get a gift, is a nice bonus.

To add to the excitement, the gift has an interesting story too, which I would like to share.

The bookmark was made out of recycled junk mail, with a cancelled stamp from Benin, by another female science blogger (woohoo!). She also has her own online crafts store: Recycled Ideas, where everything is made out of recycled material. This is a great way to find gifts to show you're giving in an environmentally friendly way.

Thank you Sciencewoman, what a great and thoughtful gift. Now if only could find time to read a book to use the bookmark with. I suppose for now, it'll have to be put to work in scientific papers.

Thursday, December 6, 2007

Holy Pasta and Authentic Sauce

The American Academy of Religion held it's annual meeting in November. And some students from the Universities of Florida and Syracuse presented their research on the church of the Flying Spaghetti Monster.

It is about time that the church of the Flying Spaghetti Monster is taken more seriously. How else are we supposed to learn about the effect His Noodly Appendages have on our daily lives?

Monday, December 3, 2007

Cephalopod tricks

I need to learn this skin-changing trick. Imagine all the naughty things I could do.

Sunday, December 2, 2007

Two down

I finally turned in my second exam. It was a strange one. The professor did not give me a deadline to complete the open-book exam, so I had to write, until I thought it was enough. But when is enough, well... enough? With six questions, rather broad in scope, there seemed to be no end to my writing. I could have written a book on each of the questions. Eventually I just gave up, and turned in what I had. Hopefully it will be adequate. I suppose I prefer a deadline. At least then I can do the best I can in the time available, and no more. The exam also had a closed-book section, so I did that on Friday. Tomorrow morning the next exam should come in. I can hardly wait... not.

F1-3 woke up this morning with a high fever and nausea. So much for working on exams today. I don't remember her ever being this cranky. She has been inconsolable for hours now, and complains that her eyes hurt. I scheduled a doctor's appointment for this afternoon. In the meantime, I serve no other purpose in life that being the hanger she has suspended herself from.

F1-3 cried for almost 3 hours straight, at which point I scheduled an appointment and took her in to see the doctor. Strep throat, accompanying rash. Antibiotics. Contagious for another 24 hours after starting meds. And to top it all off, when we changed F1-2, we noticed the same rash, and he had a slight fever. It looks like I'm home at least through Wednesday with 2 sick kids. This should make for an interesting qualifying exam.

F1-2 definitely has Scarlet fever. Just lovely. And this morning he had 4 seizures. I spent the entire morning at the doctor's office with him. My exam came in Monday night. I have a week to answer 1 question. And it's not exactly an easy question either. I haven't even had time to do a basic literature search yet. Ready, set....go!

Get a new brain

Cuttlefish is showing us a new way to get a substitute for those of us who could use a replacement. Brilliant!!

And I copy-and-paste (but you should go and check the picture at cuttle's blog):

We’ve got sweaters to mend; we’ve got socks we can darn,
So pull up a chair, and I’ll spin you a yarn;
It’s a song with a Scarecrow-of-Oz-like refrain:
Please pick up your needles and knit me a brain!

I’ve knitted my bones, and I’ve knitted my brow,
But I’ve never seen brains knitted—up until now;
With each neural pathway a separate skein,
It’s Art and it’s Science, so knit me a brain!

Two hemispheres knit, and then reaching across ‘em
A beautiful, zippered-up corpus callosum;
Such fine application of knit, purl, and chain,
I want one myself—so please, knit me a brain!

With the brain’s convolutions appropriately gyred
This fabric creation has got me inspired!
My love for this art, I can hardly contain—
So how can I get one? Please knit me a brain!

Some people may tell you I’ve gone ‘round the bend
That the stuff ‘twixt my ears needs some decades to mend.
I could use some new grey-matter; mine’s gone insane,
It would not go to waste, if you’d knit me a brain.

You can see for yourself—why, just look at the time
I must take to obsessively put things to rhyme;
Something’s wrong, and I think that the answer is plain:
I need a replacement—so knit me a brain!