QBE Lab Department of Plant Pathology UC Davis

QBE Lab UC Davis Department of Plant Pathology

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QBE Lab Blog

Cranberry diseases

posted 21 Aug 2012 10:51 by Gregory Reynolds   [ updated 21 Aug 2012 11:07 ]


The cranberry field trip was quite interesting in spite of it being scorching hot and humid outside. In addition to learning about production practices, we saw several diseases, including a severe dodder infestation, Phytophthora root rot, funky flower, and fairy ring. Fairy ring is caused by a new Helicobasidium species which, along with being a plant parasite, acts as a mycoparasite and grows on rust as an alternate host. Management of the disease may be achieved through treating weeds with fungicides, which is the first time I have ever heard of using chemical control on weeds for anything other than killing them. Very unique system.

Dodder (Cuscuta gronovii)                                        Fairy ring (Novel Helicobasdium spp.)                    Weeds filling in areas killed by Phytophthora root rot

APS 2012 Rhode Island!

posted 15 Aug 2012 08:55 by Robin Choudhury   [ updated 15 Aug 2012 09:04 ]


I just got back from my first national meeting at it was amazing! Providence was the perfect town: interesting enough to attract people, not too interesting so that people would skip sessions (*cough Hawaii cough*) . I ended up joining two committees: Epidemiology and Phyllosphere Microbiology. I enjoy epidemiology and it was nice to put faces to the names of people whom I had read, but it is a very large group and it was a little daunting to speak up (I ended up sitting quietly in a corner throughout the whole committee meeting). I joined Phyllosphere Microbiology quite by accident: I was looking for something to do on Sunday morning and wandered in to a room where Johan Leveau and a few other people were sitting, and they seemed to think I was a new member! The Phyllosphere committee seems quite a bit smaller (hardly more than a dozen) with people from all sorts of disciplines but it lets me explore my interest in ecology and food safety that have lay dormant for a while. The special sessions were really nice, I got a huge kick out of seeing both Jo Handelsman and Pedro Crous in the elevator, sadly I missed both of their talks. The technical sessions were also really nice, I enjoyed hearing more about epidemiology and mycology. All in all a very nice trip! Hopefully I can have enough work done by next March that I can attend next year’s meeting in Austin!

Thoughts from 37,000 feet

posted 3 Aug 2012 15:22 by Gregory Reynolds


I am currently on my way to the annual American Phytopathological Society meeting in Providence, RI and enjoying internet on an airplane for my first time. At the moment, we are apparently a bit north of Area 51, and I’m sipping on a Bloody Mary, so a good start to the meeting. I, along with my fellow QBEheads (who will be disappointed to see I beat them to the punch in commenting on this), will be going on the cranberry field trip tomorrow to learn about diseases and production practices for this unique crop. Cranberry is a pretty big crop in Wisconsin, so I have seen bogs before on my way in between Illinois and Minnesota, but this will be my first opportunity to get an up close look. Needless to say, I’m pretty pumped. I am also presenting a poster on my matrix population model that I am quite pleased with. This will also be my first time in the Northeast, unless you count Cleveland or North Carolina. I suppose after 26 years of life, it’s about time. I’m going to keep this short, just wanted to enjoy the novelty of surfing the web on an airplane. More to come (and pictures from the aforementioned field trip) in the near future.

Yield loss,a loss of face, and new challenges: Vignettes from QBE lab’s first 24 months

posted 19 Jun 2012 11:54 by Neil McRoberts   [ updated 30 Jun 2012 10:39 ]


It is a little over two years since cubelab opened its doors and epidemiology returned in earnest to the Plant Pathology Department at UC Davis after close to a 10 year absence.  After two years a clear picture of what cubelab is all about is starting to emerge and I’m excited by the challenge of developing the area of science where plant disease epidemiology, in the traditional sense, meets the social sciences.  As the practicalities of feeding the human population within the environmental limits of the planet continue to challenge our ingenuity it seems that integrative research of the type which I hope cubelab will do is going to be needed more than ever. Paul Esker (University of Costa Rica), Serge Savary (INRA, Toulouse) and I have just submitted a review of crop loss analysis methods in which we have tried to pull the academic side of the subject back from a focus on the gap between actual yields and theoretical yields to consider the more pressing problem of the gap between actual yields and required yields.  The paper has only just started making its way through the peer review process but will hopefully be published by CABI later in the year in their review journal

I have collaborated with Paul and Serge for many years while we have been located in various places around the world (always three different places!) including Iowa, northern France, Scotland, Wisconsin, Bordeaux, The Philippines, Brazil, California, Costa Rica and Toulouse.   It has been helpful in relocating from Scotland to California to have on-going collaborations which have always been conducted mostly via email.  The physical disruption has had a much smaller impact on those pieces of work than on field work, for obvious reasons.  Some of the new collaborations I have started are also making use of the internet to allow interaction-at-a-distance.  One of these new collaborations is a blog which I’ll be writing with Louis Warren of the History Department at UC Davis on a range of topics focused on the Salinas area as an historical center of food production and agricultural innovation.  Louis has just started a year-long sabbatical in Germany and at Princeton, so co-blogging seems like a potentially useful way to work together even though we won’t actually be in the same place.
 From a standing start 2 years ago, cubelab now has projects involving salad greens, processing tomatoes, grapes, citrus and Monterey pine.  To be able to work on such a diversity of host plants is one the most enjoyable aspects of being a plant disease epidemiologist in California.  Of course there are challenges too; some of them unexpected.  Back in the old country it used to be the case that my biggest worry when sampling crops in the summer was whether the water in the wheelings between carrot beds would over-top my wellies:

Summer 2009 sampling carrot fields in Perthshire, Scotland for sclerotinia germination.  Typical temperature 60-65F and overcast. And the worst thing I had to deal with was the fact that it used to take a lot longer to sample the fields after a couple of days of rain turned the alluvial soil into boot-sucking mud.  The most embarrassing thing that could happen was falling over and getting soaked, or walking out of stuck boots (I did both).
Contrast that with summer 2010.  Sampling processing tomato crops in Yolo county CA.  Typical temperature 95-100F and clear blue sky;  my first trip to sample for TSWV and collect sticky cards so that the wonderful Dr Ozgur Batuman could count the trapped thrips.  I stepped casually out of our air-conditioned car into the heat, sauntered off along a bone-dry wheeling and noted, somewhat to my surprise, a largish (it seemed to me) snake heading in the opposite direction in the wheeling on the other side of the crop bed.  “Hey Ozgur”, I shouted, “there’s a snake heading your way, quite fast.” Ozgur was leaning on the car for balance while he changed his footwear.  His head snapped up. “Where? He started scanning the field in front of him.   I pointed to the snake.  “Oh no” Ozgur said (or at least that’s what he meant), and bending down he scooped up some clods of hard, dry earth and started throwing them at the snake.  “It’s coming for the car.” Ozgur told me, arms whirling, firing a barrage of stones and earth snake-wards.  “It’s the biggest one I’ve ever seen in the wild”, I said, “but it looks a bit small to swallow the car”.  Ozgur was not impressed by my humor. “For the heat” he informed me.

And sure enough, emerging from the edge of the crop, the snake shot across the six feet of bare earth to the car (rounding Ozgur in the process) and promptly disappeared under the front and up into the engine compartment.  Now, there’s at least one good reason why a Scotsman and a Turk shouldn’t be allowed to do field work in California without a local to act as a guide: we have/had no idea about the local wildlife.  Ozgur and I didn’t want to drive off with  a snake in the engine lest it find its way into the passenger compartment and appear at our feet (and for anyone who thinks that wouldn’t be possible, the snake did eventually exit the car by just that route) grumpy, shaken, and ready to bite toe.   The snake was eventually encouraged to leave the car by a couple of field workers, but not until long after our day’s sampling schedule was  gone.  As the snake slid off to find somewhere quieter to curl up, one of the field hands calmly bent down, picked it up and carried it back to us, offering it to us as a prize.  We said “No thanks” (at least that’s what we meant).   He shrugged and put it back on the ground.  “It’s a gopher snake” he said; “completely harmless”.  Stupid? Who felt stupid?  Of course, once I knew it was harmless I was all for a photo shoot.  Despite snake delays and other practical issues, the collaboration on monitoring and forecasting thrips/TSWV for Central Valley tomato growers is coming along nicely.

Writing Papers

posted 31 Jan 2012 11:52 by Kari Arnold


In my final year as an undergraduate at UNL, I participated in a PepsiCo funded research grant program called UCARE (Undergraduate Creative Activites and Research Experience).  Under this grant, my adviser and I devised a “short term” study on cropping systems on Ky31 turf type tall fescue.  I spent hours setting the project up (cleaning then planting tree tubes with sand and grass seed), hours fertilizing and irrigating (and setting up a drip system later because this made it far more simple), hours trimming treatments based on the level of grass harvested and placing the harvested tissue in bags labeled based on treatment and date, and even more hours drying and weighing these dried samples for an end total of grass matter harvested.  Then I spent hours calculating data, making graphs and producing a poster for the UCARE showing, which was a requirement for the grant.  I never did publish that data, although I still have the poster, but now as I am working on my first publication I am getting a real feel for what it takes to WRITE a paper.  Hours….endless hours…go into research and these hours (more like months/years) most times equate into a poster, or a paper, and unless you have done work in research you just have no idea how much time you consume while trying to find what many philosophers refer to as “The TRUTH”.  I looked at that poster, which the nerdy side of me hung on my wall with pride for the entire following summer, and just thought to myself, “Wow, all that for this…..a bloody poster…..”, my nerdy self is a somewhat British/Aussie type (I don’t know where the term “bloody” was actually officially used in that context, perhaps it was Scotland…..).  So what exactly am I getting at?  The fact that it can be rather tasking on the writer/researcher/poster maker to do all of this endless work for 5 freaking pages of script or one rather large power point slide attempting to justify that what you allowed your life to be consumed by is really important and a good reason to get paid……  The “TRUTH” is there is a lot of work that goes into publishing a paper, perusing through endless journals claiming results that are either indiscreet, insignificant or unrelated to your research, then justifying their results based on their methods, just so that you can get through the introduction!  In the research world, the saying follows close behind me “Publish or Perish”, but the funny thing is, I have learned so much I didn’t know before, and I guess that’s why people call researchers of their fields “experts” because they are the only ones willing (and or crazy enough) to read all these publications related to their work :).

Mad Science

posted 15 Dec 2011 14:21 by A.J. Campbell   [ updated 15 Dec 2011 14:25 ]


My first quarter as a grad student has ended, the finals are done and I have begun to understand a little more about what a plant pathology grad student does. Parts of it are just like in the movies; movies about mad scientists who cackle ominously as they tinker with glass tubes and flasks. It is seemingly paradoxical that in the business of managing and reducing plant disease, I have intentionally killed every plant I’ve come in contact with yet.

    The intro plant pathology class is great for this. There are so much more interesting ways to kill plants than just letting them dehydrate! You can torture them in all kinds of fascinating and enlightening ways before they eventually kick the bucket. I have infected plants with viruses, oomycetes, bacteria, and fungi and seen the lovely symptoms that result. With some of these pathogens, the poor plant never had a chance and didn’t even see it coming- those are the most fun to observe because they are in the worst pain condition.  

            There is so much I’ve learned about plant pathogens and how they infect their hosts that I sometimes marvel that there are any healthy plants out there at all. Studies in plant disease have a tremendous potential impact on the world, seeing as human beings tend to like, and even need, to eat food. However I have also learned that mad scientists are not so far fetched, they exist- right here in Davis. Now I need to go put on my radiation goggles and get back to my elaborate scheme to create the ultimate carnivorous plant experiments.

Looking Up

posted 6 Dec 2011 15:23 by Kari Arnold   [ updated 6 Dec 2011 15:25 ]


When I was taking a creative writing course many moons ago, we had contemporary writers visit the class about every few weeks or so.  One gentleman stood out to me, Ted Kooser, he said people always asked him where he got his ideas from for poems, his response was always “Just look up.”  Of course those questioning him would give him a funny look, with the appearance of misunderstanding, so he offered the challenge, “Notice six things each day, I mean really take the time to stop and SEE them, you would be surpirsed what you have been missing out on.”  His words still ring through my head every time I take a walk, ride my bike, or, like this weekend, when I dropped the top on my Miata and cruised through wine country, cutting up over the Sonoma coastal redwoods to blow kisses to the Pacific on Highway 1.  The funniest thing awaited my passenger and I, to our surprise when we pulled off the road to take in the sunset on the water, we heard the thumping and bumping of drums.  Only one other person was at this stop, literally right off the beaten two lane concrete path, and in tow was his truck and a drum set.  Now I am fully aware of the time and dedication it takes to set up a kit, being a drummer myself, so there was definitely some work involved and possibly some engineering on finding a flat spot to set up said drumset.  Yet there he sat, bump, thump, thumping as the sun sunk slowly behind the water, and I thought to myself, “Wow!  Brilliant!  Gutsy! (it is the rainy season)  I have got to try this!”  I wanted to give him a high five, but I couldn’t disturb the artist heavy in his craft.
We put the top back up to break the chill and stopped off the road again for Mexican style seafood, crabcakes, crab enchiladas, and fish tacos-likely the best food I will ever have the pleasure of eating in my lifetime, of course seafood and Mexican-how could you go wrong right?  Driving back wasn’t all that bad, given it was half the drive of getting to the coast, I took every windy wooded road I knew of to get there.  I still day dream about the redwoods towering above me, finding it difficult to follow the road since the top was down and my eyes were on the trees.  There is a whole world out there that we never perceive because it isn’t in our eyes’ view.  I have never found so many mushrooms until last week when our class went mushroom hunting–it’s not that they weren’t there in the past, I just wasn’t looking for them.  I had such a crazy time just driving through the coastal mountains and vineyards and I can’t stop thinking to myself, what if I didn’t go?  Think of all the things I would have missed, the drummer, the sunset, the fall color of the hidden vineyards and the barren trunks of the grapevines who were in the heavy wind’s way, the lichens growing in the trees and blowing in the breeze, and all I had to do is look up.

Making sense out of wingdings

posted 21 Oct 2011 14:34 by Gregory Reynolds


I have spent the last couple months gathering Pinus radiata demographic data on the Monterey peninsula and used these measurements to develop a matrix population projection model for this tree species. The drive is a good three hours or so with decent traffic, so it generally makes sense to do overnight trips, and when we do, we have the good fortune to get comped rooms at The Inn at Spanish Bay. Something about spending days traipsing around in the beautiful Monterey forest and then staying nights in a ridiculously fancy inn on the shore of the Pacific Ocean with a lone bagpiper patrolling the grounds, fireplaces and robes in every room, and glasses of scotch that cost upwards of $100 makes the “job” feel less like work than anything I’ve ever done. Hopefully this will be typical for my future career in research.

Through working with Neil on our matrix model and taking a course on dynamic modeling in biology, I am slowly starting to figure out how to read papers on modeling.  The kind of papers with an average of 30 equations per page, each of which looks to the untrained eye something like a series of characters in the good ol’ wingdings font. It’s an interesting feeling, because I used to get to the equations and just basically shut down mentally until I got to the next block of text. Now I can actually make sense of what I’m looking at. Feels like I’m only a hop, skip and jump away from viewing the world in a kind of Terminator fashion where everything is digitized and broken down into equations before my eyes. And once that happens, watch out Sarah Connor!

Could do better, must try harder

posted 19 Oct 2011 15:15 by Neil McRoberts


As I was limbering up mentally for the day ahead today, curiosity took hold of me and I put the following terms into a standard Google search: “plant disease policy”.  The results were, well, frankly, maddening, and on reflection, shaming.  Take a look for yourself:

Ignoring the section inviting us to look at scholarly articles1 on the search topic, the items on page 1 are a mixture of references to journal editorial policies, web use policies (for a plant pathology department), library collection development policies (for two different plant pathology departments) and six references either directly or indirectly to a single piece of policy-relevant research on plant disease.  This single piece of work is part of the UK Government-funded flagship programme of policy-relevant research on the Rural Environment and Land Use (RELU, see http://www.relu.ac.uk/ ).  That’s it.  No USDA pages. No NSF pages. No EU pages. No FAO pages. No WHO pages; but also no hits on US university web pages either (including my own I hasten to add).  Apparently plant disease isn’t on the policy radar; or at least it doesn’t light it up enough for anything to appear on page 1 of the Google search.  Is the near-absence of a high-profile connection between policy and plant disease from Google space explainable by plant disease having no consequences for important policy areas?  No, it isn’t.  No-one would consider food security an unimportant policy area.  Here are some figures from the excellent review of global crop losses published by Erich-Christian Oerke in 20062.

The values combine the percentage potential losses to pathogens and viruses reported in Table 1 in Oerke’s paper.  For these 5 major crops, the central tendency of estimates for potential losses across 19 regions range from just over 12% in maize to nearly 30% in potato.  For rice, the crop which feeds the largest number of the world’s poor, the figure is a little over 15%.  There is nothing inconsequential about that.  So, no, if policy and plant disease don’t combine often enough in cyberspace to make it to the top of a Google search it’s not because plant disease doesn’t matter to important policy considerations.  So why is it?

We could make some easy excuses based on the arts-science schism, point out that policy-makers and their staff tend to come from one side and while we’re on the other, shake our heads ruefully at the problem of getting science onto the policy agenda, and leave it there.

Figure 1.  Data extracted from Table 1 in Oerke (2006) indicating potential 
percentage global crop losses toplant diseases for five important food crops.
We could, but I don’t think we should, for the simple reason that excuses of that sort smell as bad as a blighted tattie.  If the importance of plant disease has escaped policy-makers it’s more likely to be because we (that is, plant pathologists) have done a bad job of explaining it to them.  A worrying story which emerged from Oerke’s analysis of the global picture on crop losses is that as attainable yields have increased, potential percentage losses to disease have also increased; simply put, the more we grow the bigger the fraction we stand to lose, and have lost.  Plant diseases represent an on-going drain on food production which reduce the value of every unit of wealth invested in increasing attainable yield in disease-free plants.  Since Oerke’s figures are summaries over a large number of studies and sources of information they represent our best guesses as to what the future of crop losses will look like.  Unless something changes qualitatively the wise bet would be that losses to disease are likely to be somewhere in the region of 15%, as a global average.  Not only is that bad news for millions of people in relation to food supply and livelihoods, it also represents an inefficiency in research investment targeted purely at increasing yield.
1I love the way Google refers to the academic literature as “scholarly articles“.  It always brings into my mind images of hushed, wood-paneled libraries; work tables piled with jumbles of books and papers; silent heads bent in serious scholastic endeavours, oblivious to dust motes circling and glinting overhead in the sunlight slanting through high, mullioned windows.  It’s a romantic picture of a world that is about as close the reality of research for most of us as policy on plant disease seems to be the reality of its impact on food supply.
2Oerke, E-C. 2006.  Crop losses to pests. (Centenary Review).  Agricultural Science, 144:31-43.

Epidemiology in a George Romero Sort of Way

posted 5 Sep 2011 11:38 by Robin Choudhury   [ updated 6 Sep 2011 10:07 by Neil McRoberts ]


While wandering through a garage sale this weekend I passed by some Halloween costumes that reminded me of a post I have been meaning to do for a while.
Although my interests and the interests of this lab tend to lean towards plant epidemiology, every once in a while I run across a paper that catches my interest in other fields. Although this normally takes the form of animal or human epidemics, I recently ran into a paper that covered a more supernatural epidemiological phenomenon: zombies.
Four researchers out of Canada recently published a paper assessing epidemiological approaches to a hypothetical zombie outbreak (http://mysite.science.uottawa.ca/rsmith43/Zombies.pdf).
Zombies (for those who can actually sleep at night) are fictitious supernatural undead humans. They rise from their graves to feed on the living, and have found a healthy home in Hollywood with recent movies ’28 Days Later’, ‘Dawn of the Dead’ and ‘Zombieland’. Once a person is bitten, they slowly turn into a zombie themselves, and seek out more humans to infect. Using Hollywood movie rules, the researchers asked the question “what is the best strategy to deal with these undead fiends?”
They modeled what would happen if there were strict quarantines, a cure, or impulsive forceful attacks.
They found that even strict quarantines were rarely effective, even if they could be practiced effectively in real life. A cure would result in a zombie/human cohabitation, with the large bulk of the population being infected. Their only effective strategy? Immediate and aggressive assault.
Although based in science fiction, this paper illustrates important notes on epidemiology that can be applied in a broader sense. It illustrates the importance of close monitoring of virulent pathogens, as well as the necessity of aggressive and immediate control measures to prevent outbreaks of a virulent pathogen in a susceptible host, either plant or human. It also highlights the vast difference between a protective and an eradicative measure, and some of the weaknesses of quarantine programs.

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