Wednesday, April 23, 2008

Recent requests for help

I recently received two e-mails from some colleagues asking for some help in not so explored plant flow cytometry subjects.

You can see their messages below and if you have can give them any feedback to their question, they will certainly be very grateful.

E-mail 1:
"Dear all,

One groups wants to separate Lolium nuclei from the organelles... This project is really challenging for me and I'll need some help.

The main target is separating mitochondria (urgent application) and the second target is sorting chromosomes. Lolium has 7 chromosomes in the haploid set. As I told you I'm a little bit out of the Botany field now and I would like to come back... Do you have some protocols, procedures, papers, information, tips and tricks... that could help me? For analysis I think I shouldn't have big problems because of the equipments that I've in the lab, but for sorting I could be limited because I've a FACSAria and it has a 70 and a 100 um nozzles.

Nevertheless, probably the higher restriction for chromosome sorting it could be that instead of a UV laser the Aria has a violet laser...

Any help will be very welcome.

Kind regards,

Dr. Alfonso Blanco Fernández (e-mail:
Flow Cytometry Core Facilities
UCD - Conway Institute of Biomolecular & Biomedical Research
University College Dublin,

E-mail 2:
"Hello Joao,

Please can I have a question – do you have an experience in plant cell sorting based on neutral lipids content – ideally using auto-fluorescence. We have a customer who is sorting algae and cyanobacteria based on neutral lipids content – and asked us for an advice in this..


Roman Navratil , Ph.D. (e-mail:
Applications Specialist
iCyt Mission Technology, Inc.

Your help is needed! You can reply to these problems either by commenting this post or by contacting directly the researchers through the e-mail given in each message.

Wednesday, April 16, 2008

The Annals of Botany Plant Genome Horizons Special Issue

As it was premiered in the blog 2 and 1/2 months ago, the Annals of Botany has just released a Special Issue dedicated to Plant Genomes in tribute of Michael Bennett's, a leading researcher on this area that decided to retire from the Jodrell Laboratory (Kew Royal Botanical Gardens, UK) in 2007.

As expected this is a very interesting issue of the Annals of Botany, that covers very different topics of plant genomes and opens future horizons. The issue is composed by a nice introduction that explores the contribution of Michael Bennett (in the picture) to Genome Research, some reviews and several research papers.

It is definitely worth reading.

Sunday, April 13, 2008

Contribution area of the FLOWer database is available

Finally the contribution area of the FLOWer database is up and running. By this way you can help us to improve the database by providing either the pdf file or the reference to any of the missing articles.

Many thanks in advance for your important contribution for the improvement of the database.

European Cytometry Network Meeting report

The EMBL Flow Cytometry Core Facility has just posted the report of First European Cytometry Network Meeting (28-29th February 2008) that I've been talking you about recently on the blog. It is a very interesting reading on the expectations of the participants of the meeting. It also provides a current state of the community.

Download the report

The main developers of the network, Andy Ridell and Alexis Gonzalez, are still open to your feedback, so you can get access to the survey that was made in here. After filling it you can send it to:
Flow Cytometry Core Facility
EMBL Meyerhofstr. 1,
Heidelberg D-69117

Enjoy your reading! By the way in the picture you can have an idea of the countries represented in the European Network Cytometry Meeting.

Wednesday, April 09, 2008

Oxalis genus in South Africa

In order to highlight some of the current interests of the Facilities of Flow Cytometry in Prague and Pruhonice (Czech Republic), I will post some illustrative posters that were prepared and designed by Jan Suda.

Let's start with the poster (click on the image to have a full screen view) regarding the studies of ploidy level and genome size that we have been conducting in the Oxalis species from South Africa.

Monday, April 07, 2008

Update of the FLOWer database

We are developing great efforts to put the FLOWer database working as we wanted. After having some problems with the first version of the database, a new version is being implemented and today it is finally possible to search by Family, Genus and Species. It is a great improvement as these are some of the most important fields that a researcher may want to search when consulting the database. Other small changes have also been made, such as sorting by columns on the "Search Results", and some formatting issues on the "Articles Details" sections.

Soon, we expect to have the Contribution area finished, and then you can help us more actively by providing the reference to missing articles on the database.

We will post any more relevant updates when it is convenient.

Thursday, April 03, 2008

Late-breaking submissions on ISAC 2008 congress

There are still 6 days to submit an abstract to present a poster in the next ISAC Congress in Budapest (17th to 21st of May). The organization opened the late-breaking submissions until the next 9th of April, so this is the last chance to bring some of your work to the most important congress on cytometry.

I remember that this is the first time that plant flow cytometry is highly represented in a ISAC Congress. There will be a tutorial and two workshops totally dedicated to this important, but still minority field of flow cytometry.

Please read this older post of the blog for further details concerning the congress and especially the plant sciences sections.

And Budapest is also very beautiful!

Tuesday, April 01, 2008


Dear all,

From the 17th to the 22nd of August, the FESPB (Federation of European Societies of Plant Biologist) congress will be held in Tampere, Finland.Two other satellite congress will be held in parallel, the Moss 2008 and the Peroxidase 2008.
"The scientific programme of the FESPB 2008 will cover most aspects of modern plant biology. The aim is to arrange a conference with the highest scientific quality and novelty with wide international representation of experimental plant biology, from molecular biology to ecophysiology."

for more information, check the programme:
and the event homepage:

Whenever new relevant information becomes avaliable, this blog will be updated.

The future of scientific publishing... Is Thomson under fire?

In a nice editorial that came to my acquaintance, Koen Martens, the editor-in-chief of Hydrobiologia, makes a nice overview of the current state of scientific publishing world, as well as, envisaging the near future.

You can get it here: (it is of open access)

Of particular interest are the issues of the impact factors and their values (from Thomson’s ISI). Actually, it was only after reading this editorial that I realized that there are already several publications that, as I expected through my discussions with several colleagues, question the validity of these impact factors and on the excessive importance that they actually have (e.g., promotion or hiring of personel, grant applications, salary bonuses). Actually in an interesting editorial of The Journal of Cell Biology, it is questioned the validity of Thomson Scientific impact factors and the inability of the company to give the basic data used to calculate the impact factors. This editorial gives some nice insights on how this data can somehow be manipulated in order to improve a journal impact factor.

I think that most of the current problems are due to a lack of competition on this area. However, just recently some new tools are available that can provide further insights on the impacts that a specific publication is having. As presented in Nature, a free journal-ranking tool is now available through SCImago (since December of last year). It is called SCImago Journal & Country Rank database and presents a new rank called SJR, that analyses the citation links between journals in a series of iterative cycles, similarly as Google PageRank algorithm. Therefore not all the citations are considered equally, with those coming from journals with higher SJR having more weight. Also, contrarily to the two year citation window of JCR impact factors, the SJR ranking uses the last three years and the Scopus reference database.

From my initial tests this ranking seems to be very interesting, but the rooting of the current impact factors is so deep that I envisage a long period before this or other ranks can start to be considered. At least this a beginning.

You can test it in here for free:

A similar citation index is the Eigenfactor (, that despite being based on Thomson data, also uses the method behind Google's PageRank.

So, as Declan Butler said in his news section in Nature, is Thomson going to be under fire?

P.S. Many thanks to my colleague Bruno Castro (Department of Biology, University of Aveiro) for sending me the editorial that originated this post, and I hope, future discussion on impact factors.

List of recently published papers on plant flow cytometry - March

You can find in here the articles that were recently published on plant flow cytometry. We decided also to highlight one manuscript that was already published in 2007, but due to its omission from previous posts, and because of its importance, we found that it was relevant to add to this post.

This months highlight paper:
Leitch IJ, Beaulieu JM, Cheung K, Hanson L, Lysak MA, Fay MF. Punctuated genome size evolution in Liliaceae. Journal of Evolutionary Biology (2007) 20:2296-2308.

Ploidy level:
Halverson K, Heard SB, Nason JD, Stireman III JO. Differential attack on diploid, tetraploid, and hexaploid Solidago altissima L. by five insect gallmakers. Oecologia (2008) 154:755–761.

Fortune PM, Pourtau N, Viron N, Ainouche ML. Molecular phylogeny and reticulate origins of the polyploid Bromus species from section Genea (Poaceae). American Journal of Botany (2008) 95: 454–464.

Thieme R, Rakosy-Tican E, Gavrilenko T, Antonova O, Schubert J, Nachtigall M, Heimbach U, Thieme T. Novel somatic hybrids (Solanum tuberosum L. + Solanum tarnii) and their fertile BC1 progenies express extreme resistance to potato virus Y and late blight. Theoretical and Applied Genetics (2008) 116:691-700.

Thomas, TD, Chaturvedi R. Endosperm culture: a novel method for triploid plant production. Plant Cell, Tissue and Organ Culture (2008) 93:1-14.

Vogel J, Hill T. High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3. Plant Cell Reports (2008) 27:471-478.

Plant breeding
Cidade FW, Dall'Agnol M, Bered F, de Souza-Chies TT Genetic diversity of the complex Paspalum notatum Flugge (Paniceae : Panicoideae). Genetic Resources and Crop Evolution (2008) 55:235-246.