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: http://springerlink.com/content/1501276217582647/fulltext.pdf (it is of open access)

Picture taken from http://culturecat.net/taxonomy/term/32

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: http://www.scimagojr.com/index.php.

A similar citation index is the Eigenfactor (http://www.eigenfactor.org/), 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:
Ecology
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.

Biotechnology
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.

Freeware FCM software

Hello, I'm leaving the link for two freeware softwares for FCM data analysis, that are probably well known for the most of you (or maybe not):

WinMDI: http://en.bio-soft.net/other/WinMDI.html

WinMDI is a Windows application that reads most FCS 2.0 compliant files known from most cytometer manufacturers (in the year 2000); this is the latest version (2.9) developed by John Trotter.

and

Cylchred: http://en.bio-soft.net/other/Cylchred.html

Cylchred is a cell cycle analysis software, that works with histograms in FCS single parameter binary format with up to 1024 channels. So you may want to use WinMDI first to obtain this histograms. The latest version is 1.02, and was developed at the university of Cardiff.

Happy data analysis!

FLOWer database statistics - Top 10 journals of plant DNA flow cytometry

The European Cytometry Network Meeting - 2.0 Cytometry

As announced in here, last week, the European Cytometry Network meeting occurred in Heidelberg (indeed, a very nice city in Germany), and what a nice meeting it was. The hosts, Andy Riddell and Alexis Gonzalez, were excellent, as well as most of the conferences. We were also quite happy with the overall feedback on the talk that we gave (you can download it here: Plant Flow Cytometry - Heidelberg) and with the nice contacts that were made. But enough of bla, bla, and let's have a small summary of the main ideas of the meeting.

Andy and Alexis presented us with their idea of a possible European Cytometry Network meeting that would have the simple purpose of helping cytometry researchers and related scientists to get closer to each other. For that, besides other things, a proposal for creating a website 2.0 was made. For those that are not familiar with these websites, they work similarly to Myspace, Windows Live Spaces or Facebook, where each registered user can easily connect to other users, share documents, links, interests and information, enabling a straightforward communication with other members of the online community. And all these things are usually very easy to do, even for less experiences users. It is a very interesting idea and they have already designed some interesting and appealing website, that is only in need of an appropriate server.

Of course, a physical structure for the network is in discussion for the future, but more importantly the meeting intended to create some brainstorming of people's ideas and interests on such a network. So, Andy and Alexis are eager to know what are your ideas for such a network and you can contact them at the EMBL Flow Cytometry Core Facility webpage. For sure it is not intended to compete with ISAC and National Cytometry Societies, but it is rather a congregation of information that could help when requesting for funds and that could ease the contacts at European level.

We will keep you updated on the advances of the Network.

List of recently published papers on plant flow cytometry - February

This past month of February, unfortunately, not so many papers on plant flow cytometry came to our hands. Either the publication rate was lower than usual, or we were not so aware of the current contents available in this month's journals. Nevertheless you can always contribute to this topic by sending us some notice about missing publications.

Ploidy level:
Ramsey J, Robertson A, Husband. Rapid adaptive divergence in new world Achillea, an autopolyploid complex of ecological races. Evolution (OnlineEarly)

Trenchard LJ, Harris PJC, Smith SJ, Pasiecznik NM. A review of ploidy in the genus Prosopis (Leguminosae). Botanical Journal of the Linnean Society (2008) 156:425–438

Jurado S, Díaz-Triviño S, Abraham Z, Manzano C, Gutierrez C, del Pozo C. SKP2A, an F-box protein that regulates cell division, is degraded via the ubiquitin pathway. The Plant Journal (2008) 53:828–841

Perera PIP, Hocher V, Verdeil J-L, Bandupriya HDD, Yakandawala DMD, Weerakoon LK. Androgenic potential in coconut (Cocos nucifera L.). Plant Cell, Tissue and Organ Culture (2008) 92:293–302

Plant Flow Cytometry Groups - Portugal

A new section regarding the plant flow cytometry groups of each country is starting this month. A new country/region will be posted each month.

To start, and despite I am currently located in Czech Republic, the home country of the administrators of this blog was chosen: PORTUGAL

Unfortunately, so far, only a few groups in Portugal have used flow cytometry to study plant cells. Their list follows below:

Conceição Santos, João Loureiro (now in Department of Botany, Charles University in Prague, Czech Republic), Eleazar Rodriguez, Glória Pinto, Sílvia Castro - Laboratory of Biotechnology and Cytomics, Department of Biology, University of Aveiro, Aveiro, Portugal
No. of publications: 10 (1 in collaboration with Fernanda Leal and Olinda Pinto-Carnide, Department of Biotechnology and Genetics, University of Trás Montes & Alto Douro, Vila Real, Portugal)

Maria Lima and Maria Candeias - National Agronomic Station, Department of Plant Protection, Oeiras, Portugal (flow cytometry with collaboration of Artur Paiva, Centro Histocompatibilidade do Centro, Coimbra, Portugal)
No. of publications: 1

Augusto Peixe - University of Évora, Évora, Portugal (flow cytometry services provided by the Plant Cytometry Services – Schijndel, The Netherlands)
No. of publications: 2

Ana Delauney Caperta - Centro de Botânica Aplicada à Agricultura, Instituto Superior de Agronomia, Universidade Técnica de Lisboa, Lisbon (flow cytometry with collaboration of Armin Meister, IPK, Department of Cytogenetics, Gatersleben, Germany)
No. of publications: 1

Flow cytometry core facilities in Portugal:
Cell Imaging Unit - Instituto Gulbenkian de Ciência, Lisbon (Responsible for all flow cytometry services: Rui Gardner)
Flow Cytometry Unit - Institute for Molecular and Cell Biology, Porto (Responsible: Simon Monard)
Flow Cytometry Unit - Institute of Molecular Medicine, Lisbon


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Reference list:
Caperta A. D., Delgado M., Ressurreicao F., Meister A., Jones R. N., Viegas W. & Houben A. (2006): Colchicine-induced polyploidization depends on tubulin polymerization in c-metaphase cells. – Protoplasma 227: 147-153.

Castro S., Loureiro J., Rodriguez E., Silveira P., Navarro L. & Santos C. (2007): Evaluation of polysomaty and estimation of genome size in Polygala vayredae and P-calcarea using flow cytometry. – Plant Science 172: 1131-1137.

Castro S., Loureiro J., Santos C., Ater M., Ayensa G. & Navarro L. (2007): Distribution of flower morphs, ploidy level and sexual reproduction of the invasive weed Oxalis pes-caprae in the western area of the Mediterranean region. – Annals of Botany 99: 507-517.

Conde P., Loureiro J. & Santos C. (2004): Somatic embryogenesis and plant regeneration from leaves of Ulmus minor Mill. – Plant Cell Reports 22: 632-639.

Greilhuber J., Temsch E. & Loureiro J. (2007): Nuclear DNA Content Measurement. In: – Dolezel J., Greilhuber J. & Suda J. (eds) Flow cytometry with plant cells. Wiley-Vch Verlag, Weinheim, pp 67-101.

Leal F., Loureiro J., Rodriguez E., Pais M. S., Santos C. & Pinto-Carnide O. (2006): Nuclear DNA content of Vitis vinifera cultivars and ploidy level analyses of somatic embryo-derived plants obtained from anther culture. – Plant Cell Reports 25: 978-985.
Lima M., Paiva A. & Candeias M. I. (2003): Flow cytometry - a simple method for nuclear DNA content evaluation of Vitis vinifera cv. Periquita somatic embryos obtained from anther cultures. – Vitis 42: 99-100.

Loureiro J., Pinto G., Lopes T., Dolezel J. & Santos C. (2005): Assessment of ploidy stability of the somatic embryogenesis process in Quercus suber L. using flow cytometry. – Planta 221: 815-822.

Loureiro J., Rodriguez E., Costa A. & Santos C. (2007): Nuclear DNA content estimations in wild olive (Olea europaea L. ssp europaea var. sylvestris Brot.) and Portuguese cultivars of O. europaea using flow cytometry. – Genetic Resources and Crop Evolution 54: 21-25.

Loureiro J., Rodriguez E., Dolezel J. & Santos C. (2006): Comparison of four nuclear isolation buffers for plant DNA flow cytometry. – Annals of Botany 98: 679-689.

Loureiro J., Rodriguez E., Dolezel J. & Santos C. (2006): Flow cytometric and microscopic analysis of the effect of tannic acid on plant nuclei and estimation of DNA content. – Annals of Botany 98: 515-527.

Loureiro J., Suda J., Dolezel J. & Santos C. (2007): FLOWer: A plant DNA flow cytometry database. In: – Dolezel J., Greilhuber J. & Suda J. (eds) Flow cytometry with plant cells. Wiley-VCH, Weinheim, pp 423-438.

Peixe A., Barroso J., Potes A. & Pais M. S. (2004): Induction of haploid morphogenic calluses from in vitro cultured anthers of Prunus Armeniaca cv. 'Harcot'. – Plant Cell Tissue and Organ Culture 77: 35-41.

Peixe A., Campos M. D., Cavaleiro C., Barroso J. & Pais M. S. (2000): Gamma-irradiated pollen induces the formation of 2n endosperm and abnormal embryo development in European plum (Prunus domestica L., cv, "Rainha Claudia Verde"). – Scientia Horticulturae 86: 267-278.

Pinto G., Loureiro J., Lopes T. & Santos C. (2004): Analysis of the genetic stability of Eucalyptus globulus Labill. somatic embryos by flow cytometry. – Theoretical and Applied Genetics 109: 580-587.