Petra Holišová’s visit

Petra arrived in Helsinki one week ago and will stay for another two weeks. She gave an informal presentation about her PhD project, showing results from her experiments on the effect of a dynamic light regime on the rate of CO2 assimilation in beech and spruce. She has been playing with our Walz GFS-3000 gas-exchange system and our RGB LED light sources. She is now doing more systematic measurements on beech seedlings.

Prof. Ariel Novoplansky’s visit

Prof. Novoplansky will arrive tomorrow and stay in Helsinki until Saturday.

He will give a talk on Monday 13 September at 15:15 titled “Ecological implications of plant communication”. (INFO building, lecture hall 2)

Knowing his earlier work, and having heard from him about current work in his lab, this promises to be a very very interesting talk.

Some key papers from Ariel’s lab:

Shemesh, H., A. Arbiv, M. Gersani, O. Ovadia, and A. Novoplansky. 2010. The effects of nutrient dynamics on root patch choice. PLoS ONE 5.

Novoplansky, A. 2009. Picking battles wisely: plant behaviour under competition. Plant Cell & Environment 32: 726-741.

Falik, O., Reides, P., Gersani, M. and Novoplansky, A. 2005. Root navigation by self inhibition. Plant Cell & Environment 28: 562-569.

Gruntman M, Novoplansky A. 2004. Physiologically-mediated self/nonself discrimination in roots. PNAS 101: 3863–3867.

Spectroradiometer

I am evaluating specifications of array detector spectroradiometers.
In the literature one can see them used sometimes for measuring UV-B in sunlight or in UV-B supplementation studies with plants. These single monochromator instruments are not good enough for this. They can overestimate erythemal doses by 100% or more in some cases. So, be careful when reading papers! The most popular brand is Ocean Optics. They are good for visible light measurements. However, with special measuring and calibration procedures they could be used to measure UV-B. I have not seen these special calibrations applied in research with plants, only in the recent methodological literature. I became aware of these from a reference sent to me by Prof. L.O. Bjorn, and investigating this possibilities is also part of the work of one of the technical work groups of the COST action UV4growth. One of the experts on this type of calibration is here in Helsinki, at STUK. I will contact him.

Continue reading “Spectroradiometer”

Minutes of Lab Meeting 25th August

We had a project meeting on Wednesday 25th August. Pedro, Matt, Titta, Luis, and Fang were present. We all briefly reported on our work progress since the last meeting. We also talked about coming activities.

  1. Fang and Luis will give posters at the SPPS meeting for PhD students in Espoo next week.
  2. We will meet with Prof. Gareth Jenkins (Glasgow University), UV researcher at a molecular and signalling level, on Friday 3rd September in the morning in Espoo. (He gives a talk on Thursday afternoon.)
  3. Pedro had to skip participation in UNEP meeting because he is not fully recovered from the operation in his foot.
  4. UV4growth COST work groups’ meetings delayed because of delayed signing of contract and start of activities.
  5. The CEO from a LED lamps company will come and talk with us at 9.00 am on 2nd September about possible collaboration.
  6. Luis will go to Talin to the Plant Biology meeting. He will not give a presentation, but will report back on what the other groups are doing.
  7. Prof. Ariel Novoplansky will come during the week of 13-18th September and talk at the seminar series on 13th Sept (Monday). We will have a research group dinner with him on Tuesday evening. In preparation for his visit, each of us will read one of his research papers and report back. Some papers to choose from were attached to Matt’s e-mail and for others follow the link. They go on a first come first served basis. http://www.bgu.ac.il/desert_ecology/Novoplansky/hp.htm#publications
  8. A Czech PhD student called Petra Holišová working with Matt’s collaborators in Brno will visit on an exchange to do some research into stomatal response to coloured light from 18th September (?).
  9. Matt will give a presentation at a symposium on water relations in Cartagena, Murcia,Spain, during the first week of October.
  10. Pedro will start teaching for the semester on 6th September – Plant Physiological Ecology.
  11. Titta will do a pedagogy course and I will do a teacher training course this term.
  12. Luis will take a student from the lab tech training courses to help him with genen expression and phenolic analysis from October to December.
  13. We will buy a spectro-radiometer for the group.
  14. Pedro and Fang will make another light source for the GSF now, and another two or three a little bit later. We will build a blue light source (435 nm peak), another RGB source, and a red and a far-red source, and possibly a pure green one later. We will have built at the workshop a nicer skirt/light mixing chamber to put between the LED sources and the cuvette.

Titta’s latest paper is on-line

The reprint of Titta’s latest paper “Seasonal fluctuations in leaf phenolic composition under UV manipulations reflect contrasting strategies of alder and birch trees” by “Titta Kotilainen, Riitta Tegelberg, Riitta Julkunen-Tiitto, Anders Lindfors, Robert B. O’Hara, Pedro J. Aphalo” is available at http://onlinelibrary.wiley.com/doi/10.1111/j.1399-3054.2010.01398.x/pdf, as it has been published on-line in Physiologia Plantarum.

More R stuff

Some weeks ago I wrote a post about ggplot2, an R package for plotting. I have been playing with it for some time, and it tends to be much simpler to use than lattice, which we have been using lately. However, it tends to lack a bit of flexibility, as it is less mature than lattice. So, for relatively simple figures I would use ggplot2, but for more complex ones, I think that right now lattice offers more flexibility, at the cost of more complex commands. There is also the package latticeExtra that adds even more flexibility to lattice.

Today I came across the package latticist which adds a GUI for plotting with lattice. One creates the plot interactively using menus and the system displays the plot and the R code used to create it. It has different GUIs based on different code libraries. The one based on the playwith package seems to be the nicest one. The latticist web page gives more information and some screenshots. The person behind this package is Felix Andrews. Installation is a bit complicated as the GTK+ library needs to be installed. Under Windows this happens more or less automatically (one has just to agree to it being installed) but may need administrative rights (I am not sure about this, I did install from an account with administrative rights under Windows 7). I think the effort to get it installed if worthwhile.

An example lattice plot created using latticist