Tag Archives: tomato

Tomatoes On My Mind

I’ve got tomatoes on my mind, so summer must be coming. It seems every where I turn, I’m being reminded of tomatoes. Not the grocery store/hot house kind, but the fresh farmer’s market/back yard-grown kind with juice and flavor so plentiful that it runs down your arms and onto the sunny porch floor where you are having your lunch. At first it was just from my dad that I was hearing about tomatoes. He is an avid gardener, but lives ‘up North’ where the growing season is wedge in between the edges of winter. And although they’ve been having frost until just lately, he’s been reading about vertical gardening (to optimize land usage) and dreaming of his crop of tomatoes.

I guess I haven’t been helping his insanity any with the garden catalogs I share with him, or my tales of season here in the ‘sunny South’. But it seems it isn’t just Dad & me now – the insanity seems to be spreading. Last week the Sunday paper ran a story on bread salads & featured a tomato salad – I am glunking (as it is known in my family) as I type because my mouth is watering at the thought of a good tomato-bread salad. My last trip to my local farmer’s market didn’t result in any tomatoes, but they were selling tomato plants.

Even my BioMed Central e-article alert is conspiring to add to my tomato dreams. As I scrolled through the list of ‘latest research articles in my subject areas’, my eye was naturally caught by the article entitled “Tomato root transcriptome response to a nitrogen-enriched soil patch“. How could it not peak my interest with my summer tomato insanity, my past experiences in expression analyses, and even a brief stint in a rhizobial lab as a technician? And I’m glad my ‘tomato affliction’ lead me to this article – it is highly accessed, well written & interesting, in my opinion. Rather than doing their experiments on well controlled, hydroponically grown tomatoes the authors instead tried to replicate a more ‘real world’ nitrogen-enrichment scenario by using an apparatus to deliver a non-homogeneously localized dose of nitrogen (as often occurs during actual fertilizer application)  & then tracking the transcriptional response of the plants to it. I don’t know that I found any of the the publication’s results surprising, or unexpectedly enlightening, but I did like the way they did their controls & experiments. I also really liked the way that they explained their experiments. If you take a look at the paper (it is free to access), check out figure 1a. Some might say that the image is simplistic, but it so perfectly explains the key aspect of the experiment – what I called the ‘non-homogeneously localized dose of nitrogen’ which isn’t all that specific of a description on my part. In an instant this simple image endows so much understanding to the reader – there is no extraneous jargon, verbiage,  or detail to slow one’s comprehension of the meaning. Figure 1a is elegant because of its simplicity and ease of absorption, in my opinion. This level of presentation is rare in research publications, which are often so dry that to all but the most interested they are a plow. Why is simplicity so valued in ‘little black dresses’, but not communication? (Sorry, I’ve digressed from my tomato insanity to a different bee in my bonnet – I’ll try to get back on track…)

If you too are dreaming of summer vacation & all that it might have in store, check out the article cited below for a science geek bite of fresh tomato & ENJOY!

ResearchBlogging.orgRuzicka, D., Barrios-Masias, F., Hausmann, N., Jackson, L., & Schachtman, D. (2010). Tomato root transcriptome response to a nitrogen-enriched soil patch BMC Plant Biology, 10 (1) DOI: 10.1186/1471-2229-10-75

Tip of the week: Sol Genomics Network

sol_genomics_networkAside from a short stint at the ASHG meeting, where it is all about the human genome with a smidge of attention to the microbes that hang around with us, I’m back and I’m focusing on plant resources again.  Recently I began to explore the Sol Genomics Network site, and that will be the focus of this tip of the week.

Sol Genomics Network focuses on “Solanaceae as model system for diversity” as they describe themselves.  And they aim to link genotypes to phenotypes for a collection of plant species.  Currently species information found at this site include: tomato, potato, eggplant, pepper, petunia, tobacco, and coffee.  Not all of them have browsers available here, but there are some maps for several, and there are links to other sources that may provide more information about the projects, clone collections, and additional details. They are also developing a breeder’s toolbox and they’d like to have some feedback on the needs of the community on that.

We will take a look at their tomato browser today, which is implemented in GBrowse, the Generic Genome Browser from the GMOD project tool kit that supports so many species and data types–and if you want some help using GBrowse you should see our freely available tutorial on that.

The site also include a number of outreach activities for students at varying levels–including a lab exercise for the high school level, a word find puzzle for youngsters with these species (we like puzzles here), and the fun and interactive animated series with a sequencing puzzle where you generate a small assembly with some sample BAC fragments (ok, they are really small BACs, but you get the point).   I know a lot of, ah, mature scientists who could stand to work with the concept of the assembly to grok that a bit better, actually….

Go directly to the BAC assembly sequencing puzzle here if you don’t have time for the whole tip of the week:  http://bti.cornell.edu/multimedia/puzzleComplete.html

Sol Genomics Network site directly: http://solgenomics.net/

More Solanaceae resources: http://solanaceae.plantbiology.msu.edu/

Metagenomic Resources from The National Academy of Science

Father’s Day I’m not sure how parents & metagenomics have gotten connected for me, but it seems they have.  You may remember my Mother’s Day post.  This past weekend my in-laws were visiting us for Father’s Day and a lot of the discussion involved recounting news stories about the tomato-associated salmonella outbreaks & quizzing the family biologist (me) on the subject.  Monday morning I wished our house guests a safe journey home & then checked my OpenHelix email account – to find an email from Mary telling me she had just gotten a metagenomics poster in her new issue of Nature Biotechnology.  (We always try to ‘share the wealth’ with each other, and you guys too, actually.)  The poster came with a web address, which I of course checked out.  Turns out …

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