Wednesday, September 10, 2008

Software evaluation - FlowJo

Following this year's ISAC congress I've been aware of many commercial software packages for the analysis of flow cytometric data. After attending to the FlowJo's commercial tutorial I was very curious to test it in the analysis of plant DNA flow cytometry results. But, what advantages can this powerful package (it was designed to ease the analysis of multiparametric results, besides other things) have in the analysis of simple, one to two parameters results, as it is the analysis of DNA histograms obtained from the isolation of plant nuclei? That is to say, which positive features FlowJo has that are not present in the software packages that are provided with your flow cytometer and that may improve your daily analysis of the obtained results?

Having used only a few of its huge list of features, I highlight two of them: batch operations (repetitive analyses performed on multiple samples) and output generation (e.g. easy exportation of tabular data to an excel file, for example). Both these features enable a much faster and easier analysis of the obtained results. For example, you can create the necessary regions and gating in a specific histogram (file) and then just copy those settings to all the other ones. I.e. to say that it is very easy to apply common procedures to all the files of an experiment; you should only do slight adjustments, but even this can be done in a very quick and efficient way. After all the analysis is done it is also very easy to export your results in the form of a table (among other options) to a variety of external platforms, let's say Excel, so that you can make further analysis. You can also create a workspace that contains all the files of your experiment and within the workspace several groups that may have specific assays. This enables the fast and easy organization of your files. Another interesting feature for the plant DNA flow cytometry community is the cell cycle analysis procedure. However, I've still not been able to test it appropriately.

The biggest disadvantage that I can point out is the price of FlowJo. Despite that it can be quite acceptable for the users from the clinical area, I find that it is still quite high for the users in plant flow cytometry. Another minor negative point is the somehow stylized presentation of the DNA histograms, that sometimes seem slightly better than they were when obtained using the standard software of the flow cytometer. However, the enormous array of available statistics provide you the real values (e.g. CV values) of your data.

So far, my experience has been very good and I personally recommend you to download a fully functional 30 day trial version of the software. It's quite straightforward to use, despite that I must confess that the tutorial that I attended in the ISAC's Congress proved to be very useful for a faster start. I would say that there's nothing better than to try it yourself.

Tuesday, September 09, 2008

The European Cytometry Network webpage

The webpage of the recently created European Cytometry Network (for further info click here) has been in beta testing already for several months. This may be a very useful and attractive platform created as a social network for the easy exchange of ideas and information between European scientists interested on cytometry. There's a special group exclusively dedicated to plant flow cytometry, which has already 15 members from several areas of plant sciences. So, it may be another web platform (together with the forum) for the discussion of general topics in plant flow cytometry as well as the place to pose any question or doubt related with the cytometric applications in plant sciences.

As the network works as invitation only, in case you are interested in joining us, please just send me an e-mail that I will promptly reply to you.

Make a good profit of it... it was created for you.

Monday, September 08, 2008

List of recently published papers on plant flow cytometry - June, July and August

Exceptionally, due to my recent busy times exposed in a previous post, this highlight of the recently published articles on Plant Flow Cytometry will include the months of June, July and August.

Genome size:
Thompson JN, Merg KF. Evolution of polyploidy and the diversification of plant-pollinator interactions. Ecology (2008) 89:2197-2206.

de Abreu IS, Carvalho CR, Clarindo WR. Chromosomal DNA content of sweet pepper determined by association of cytogenetic and cytometric tools. Plant Cell Reports (2008) 27:1227-1233.

Brito G, Loureiro J, Lopes T, Rodriguez E, Santos C. Genetic characterisation of olive trees from Madeira Archipelago using flow cytometry and microsatellite markers. Genetic Resources and Crop Evolution (2008) 55:657-664.

Consaul LL, Gillespie LJ, Waterway MJ. Systematics of North American Arctic diploid Puccinellia (Poaceae): Morphology, DNA content, and AFLP markers. Systematic Botany (2008) 33:251-261.

Garcia S, Canela MA, Garnatje T, Mcarthur ED, Pellicer J, Sanderson SC, Valles J. Evolutionary and ecological implications of genome size in the North American endemic sagebrushes and allies (Artemisia, Asteraceae). Biological Journal of the Linnean Society (2008) 94:631-649.

Stahlberg D, Hedren M. Systematics and phylogeography of the Dactylorhiza maculata complex (Orchidaceae) in Scandinavia: insights from cytological, morphological and molecular data. Plant Systematics and Evolution (2008) 273:107-132.

Eilam T, Anikster Y, Millet E, Manisterski J, Feldman M. Nuclear DNA amount and genome downsizing in natural and synthetic allopolyploids of the genera Aegilops and Triticum. Genome (2008) 51:616–627.

Ploidy level:
Izumikawa Y, Takei S, Nakamura I, Mii M. Production and characterization of inter-sectional hybrids between Kalanchoe spathulata and K. laxiflora (= Bryophyllum crenatum). Euphytica (2008) 163:123-130.

Skrlep K, Bergant M, De Winter GM, Bohanec B, Zel J, Verpoorte R, Van Iren F, Camloh M. Cryopreservation of cell suspension cultures of Taxus x media and Taxus floridana. Biologia Plantarum (2008) 52:329-333.

Jin SX, Mushke R, Zhu HG, Tu LL, Lin ZX, Zhang YX, Zhang XL. Detection of somaclonal variation of cotton (Gossypium hirsutum) using cytogenetics, flow cytometry and molecular markers. Plant Cell Reports (2008) 27:1303-1316.

Yang XM, An LZ, Xiong YC, Zhang JP, Li Y, Xu SJ. Somatic embryogenesis from immature zygotic embryos and monitoring the genetic fidelity of regenerated plants in grapevine. Biologia Plantarum (2008) 52:209-214

Zdravkovic-Korac S, Calic-Dragosavac D, Uzelac B, Janosevic D, Budimir S, Vinterhalter B, Vinterhalter D. Secondary somatic embryogenesis versus caulogenesis from somatic embryos of Aesculus carnea Hayne.: developmental stage impact. Plant Cell Tissue and Organ Culture (2008) 94:225-231.

Lubinsky P, Cameron KM, Molina MC, Wong M, Lepers-Andrzejewski S, Gomez-Pompa A, Kim SC. Neotropical roots of a Polynesian spice: The hybrid origin of Tahitian vanilla, Vanilla tahitensis (Orchidaceae). American Journal of Botany (2008) 95:1040-1047.

Mereda P, Hodalova I, Martonfi P, Kucera J, Lihova J. Intraspecific variation in Viola suavis in Europe: Parallel evolution of white-flowered morphotypes. Annals of Botany (2008) 102:443-462.

Schenk MF, Thienpont CN, Koopman WJM, Gilissen LJWJ, Smulders MJM. Phylogenetic relationships in Betula (Betulaceae) based on AFLP markers. Tree Genetics & Genomes (2008) 4:911-924.

Siena LA, Sartor ME, Espinoza F, Quarin CL, Ortiz JPA. Genetic and embryological evidences of apomixis at the diploid level in Paspalum rufum support recurrent auto-polyploidization in the species. Sexual Plant Reproduction (2008) 21:205-215.

Plant breeding
Martinez-Reyna JM, Vogel KP. Heterosis in switchgrass: Spaced plants. Crop Science (2008) 48:1312-1320.

Teyssier E, Bernacchia G, Maury S, Kit AH, Stammitti-Bert L, Rolin D, Gallusci P. Tissue dependent variations of DNA methylation and endoreduplication levels during tomato fruit development and ripening. Planta (2008) 228:391-399.

Cell Cycle:
Da Silva EAA, Toorop PE, Van Lammeren AAM, Hilhorst HWM. ABA inhibits embryo cell expansion and early cell division events during coffee (Coffea arabica 'Rubi') seed germination. Annals of Botany (2008) 102:425-433.

Short resume of the Xth Symposium of the International Organization of Plant Biosystematics

Before updating all the usual sections of the blog, I want to leave you a very short overview of the Xth Symposium of the International Organization of Plant Biosystematics. Overall, the Symposium was a success both in organization and scientific value. The venue was held on the beautiful High Tatras which was another positive aspect.

Flow cytometry speaking it was nice to see that there are more and more researchers using this technique to help solving byosystematic and taxonomy problems. The number of posters where flow cytometry was used exceeded the 20 and several talks also referred its usefulness and potential for large scale ploidy level and genome size analyses. The only regret was the unexpected cancelling of D. Soltis talk due to passport issuing problems. Maybe next time...

Finally, Jan Suda wonderfully and enthusiastically presented a talk addressing all the potentialities that the technique has in the field of Biosystematics, which was a sure highlight of the congress's second day.

I leave you some other pictures from the Tatras journey:

The return of the blog

Dear friends,

I know! It has been already more than two months without any posts in the blog. Since the Symposium of the International Organization of Plant Biosystematics in Slovakia that I've been most of the time out of office in several field trips for collection of Aster amellus. This beautiful daisy has been studied throughly by Zuzana Münzbergova in the Czech Republic where a secondary contact zone between two cytotypes (diploids and hexaploids) can be found. In order to understand the distribution of both cytotypes Sílvia Castro and I have been collecting this species in the neighbouring countries of the Czech Republic. So far, we have thoroughly explored the Slovak Republic and Austria, but there's still Poland to come. However, before leaving to the Polish land for the last week of field season of this year I will post the usual Articles of the Month section and one of several software highlights.