Plant Flow Cytometry

The comeback

2009-09-21T18:41:00.004+01:00

Dear friends and colleagues,

I am really sorry for my silence. The blog has not been updated for a long time (December 2008), and this is mainly due to my lack of time justified by my new position - since February 2009 I've returned to my country (Portugal), as an Assistant Professor in the Department of Life Sciences (former Department of Botany) of the University of Coimbra, and together with the preparation and giving of classes, I've been very busy with project's submission in order to obtain some funds to establish a new lab on Plant Evolutionary Biology (especially, genome evolution). To those interested, my new webpage can be found in this link.

Also, I would like to take this opportunity to say that we are looking for dynamic and enthusiastic Master, PhD and Post-Doc researchers interested in joining our young team and continuing their studies in this promising area of research. Those interested should contact me at: jloureiro@bot.uc.pt

I promise you that I will try to find some time to continue this blog and to post some of its regular sections.

The Congress and Meetings links are updated

2008-12-03T12:59:00.003Z

The links to some of the most interesting Congresses of 2009 are already updated on the side bar of the blog.

See you there.

List of recently published papers on plant flow cytometry - October and November

2008-12-02T13:24:00.013Z

As I told in the previous post, I've had limited time to dedicate to the blog. Because of that I bring you the list of the recently published papers of the two last months, October and November. There are some very interesting papers in this package... so, I wish some nice readings.

Genome size:
Palomino G, Hernandez LT, Torres ED. Nuclear genome size and chromosome analysis in Chenopodium quinoa and C. berlandieri subsp. nuttalliae. Euphytica (2008) 164: 221-230.

Robert ML, Lim KY, Hanson L, Sanchez-Teyer F, Bennett MD, Leitch AR, Leitch IJ. Wild and agronomically important Agave species (Asparagaceae) show proportional increases in chromosome number, genome size, and genetic markers with increasing ploidy. Botanical Journal of the Linnean Society (2008) 158: 215-222.

Achigan-Dako EG, Fuchs J, Ahanchede A, Blattner FR. Flow cytometric analysis in Lagenaria siceraria (Cucurbitaceae) indicates correlation of genome size with usage types and growing elevation. Plant Systematics and Evolution (2008) 276: 9–19.

Costa IR, Dornelas MC, Forni-Martins ER. Nuclear genome size variation in fleshy-fruited Neotropical Myrtaceae. Plant Systematics and Evolution (2008) 276: 209–217.

Rosado TB, Clarindo WR, Carvalho CR. An integrated cytogenetic, flow and image cytometry procedure used to measure the DNA content of Zea mays A and B chromosomes. Plant Science 176 (2009) 154–158.

Temsch EM, Greilhuber J, Hammett KRW, Murray BG. Genome size in Dahlia Cav. (Asteraceae–Coreopsideae). Plant Systematics and Evolution (2008) 276:157–166.

Ploidy level:
Ecology
Arvanitis L, Wiklund C, Ehrlen J. Plant ploidy level influences selection by butterfly seed predators. Oikos (2008) 117: 1020-1025.

Biosystematics
Singliarová B, Chrtek J, Mráz P. Loss of genetic diversity in isolated populations of an alpine endemic Pilosella alpicola subsp. ullepitschii: effect of long-term vicariance or long-distance dispersal? Plant Systematics and Evolution (2008) 275: 181-191.

Fortune PM, Schierenbeck K, Ayres D, Bortolus A, Catrice O, Brown S, Ainouche ML. The enigmatic invasive Spartina densiflora: A history of hybridizations in a polyploidy context. Molecular Ecology (2008) 17: 4304-4316.

Ricca M, Beecher FW, Boles SB, Temsch E, Greilhuber J, Karlin EF, Shaw AJ. Cytotype variation and allopolyploidy in North American species of the Sphagnum subsecundum complex (Sphagnaceae). American Journal of Botany (2008) 95: 1606-1620.

Biotechnology
Perera PIP, Perera L, Hocher V, Verdeil JL, Yakandawala DMD, Weerakoon LK. Use of SSR markers to determine the anther-derived homozygous lines in coconut. Plant Cell Reports (2008) 27: 1697-1703.

Astarini IA, Plummer JA, Lancaster RA, Yan G. Identification of 'Sib' plants in hybrid cauliflowers using microsatellite markers. Euphytica (2008) 164: 309-316.

Apomixis
Kaushal P, Malaviya DR, Roy AK, Pathak S, Agrawal A, Khare A, Siddiqui SA. Reproductive pathways of seed development in apomictic guinea grass (Panicum maximum Jacq.) reveal uncoupling of apomixis components. Euphytica (2008) 164: 81-92.

Cell cycle:
Bagniewska-Zadworna A. The root microtubule cytoskeleton and cell cycle analysis through desiccation of Brassica napus seedlings. Protoplasma (2008) 233:177–185.

Functional studies:
Zonno MC, Vurro M, Lucretti S, Andolfi A, Perrone C, Evidente A. Phyllostictine A, a potential natural herbicide produced by Phyllosticta cirsii: In vitro production and toxicity. Plant Science (2008) 175: 818–825 .

A hell of a joke on Impact Factors

2008-11-28T14:50:00.001Z

In a recent issue of Genome Biology, Gregory Petsko published a very funny commentary on impact factors. Basically, it tells the story of a recently departed genome biologist that discusses the impact factor of his life with St Peter at the Pearly Gates.

You can get it here LINK.

Wordle of the blog

2008-11-25T08:59:00.008Z

The Wordle (http://www.wordle.net/) of the blog. This utility generates word clouds from the text that is inserted. In this case the whole blog. Unfortunately I've had little time to update the blog recently. I will try to catch up soon. Sorry....

Two in a row... Another Science paper using flow sorting on plant protoplasts

2008-11-07T08:54:00.005Z

Can it be two in a row? It is indeed. Two weeks ago de Smet and co-authors published a study entitled "Receptor-Like Kinase ACR4 Restricts Formative Cell Divisions in the Arabidopsis Root" on Science. It is a very interesting application of flow sorting of plant perycicle cells undergoing lateral root initiation to identify the receptor-like kinase ACR4 of Arabidopsis.

One of the authors told me that this important and interesting study resulted from a fruitful collaboration between Philip Benfey's group from the Duke Institute for Genome Sciences & Policy, Duke University and the Root Development Group in Ghent headed by Tom Beeckman with cell sorting being done in both Departments.

Congratulations to all the persons involved in such groundbreaking investigation.

Abstract:
During the development of multicellular organisms, organogenesisand pattern formation depend on formative divisions to specifyand maintain pools of stem cells. In higher plants, these activitiesare essential to shape the final root architecture because thefunctioning of root apical meristems and the de novo formationof lateral roots entirely rely on it. We used transcript profilingon sorted pericycle cells undergoing lateral root initiationto identify the receptor-like kinase ACR4 of Arabidopsis asa key factor both in promoting formative cell divisions in thepericycle and in constraining the number of these divisionsonce organogenesis has been started. In the root tip meristem,ACR4 shows a similar action by controlling cell proliferationactivity in the columella cell lineage. Thus, ACR4 functionreveals a common mechanism of formative cell division controlin the main root tip meristem and during lateral root initiation.

Another great achievement of plant chromosome flow sorting

2008-10-15T10:42:00.009+01:00

It was with great pleasure that I received an alert of the publication of the physical map of the 1-Gigabase bread wheat chromosome 3B on the top ranking journal Science. Not only because it is another very important contribution of plant flow sorting, but mostly because I know some of the people involved on this great achievement and all the efforts that were made within this worldwide research team to achieve this outcome. To Jaroslav Dolezel and all his team my sincere greetings.

Abstract:

As the staple food for 35% of the world’s population, wheat is one of the most important crop species. To date, sequence-based tools to accelerate wheat improvement are lacking. As part of the international effort to sequence the 17–billion–base-pair hexaploid bread wheat genome (2n = 6x = 42 chromosomes), we constructed a bacterial artificial chromosome (BAC)–based integrated physical map of the largest chromosome, 3B, that alone is 995 megabases. A chromosome-specific BAC library was used to assemble 82% of the chromosome into 1036 contigs that were anchored with 1443 molecular markers, providing a major resource for genetic and genomic studies. This physical map establishes a template for the remaining wheat chromosomes and demonstrates the feasibility of constructing physical maps in large, complex, polyploid genomes with a chromosome-based approach.

List of recently published papers on plant flow cytometry - September

2008-10-03T14:23:00.009+01:00

September issues have been quite generous for flow cytometry related works... This month will contemplate 8 highlights from many different areas... A sign that flow cytometry is being more and more applied in different fields of plant sciences.

Genome size:
Fuchs J, Jovtchev G, Schubert I. The chromosomal distribution of histone methylation marks in gymnosperms differs from that of angiosperms. Chromosome Research (2008) 16:891–898.

Smarda P, Bures P, Horová L, Rotreklová O. Intrapopulation genome size dynamics in Festuca pallens. Annals of Botany (2008) 102:599–607.

Ploidy level:
Biotechnology
Lim WS, Earle ED. Effect of in vitro and in vivo colchicine treatments on pollen production and fruit set of melon plants obtained by pollination with irradiated pollen. Plant Cell Tissue and Organ Culture (2008) 95:115-124.

Weber J, Georgiev V, Pavlov A, Bley T. Flow cytometric investigations of diploid and tetraploid plants and in vitro cultures of Datura stramonium and Hyoscyamus niger. Cytometry (2008) 73A:931-939.

Biosystematics

Consaul LL, Gillespie LJ, Waterway MJ. Systematics of three North American polyploid arctic alkali grasses (Puccinellia, Poaceae): morphology, ploidy, and AFLP markers. Botany (2008) 86:916-937.

Flow sorting:
Kofler R, Bartos J, Gong L, Stift G, Suchánková P, Simková H, Berenyi M, Burg K, Dolezel J, Lelley T. Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1. Theoretical and Applied Genetics (2008) 117:915–926.

Algae physiological studies:
Li Y, Huang J, Sandmann G, Chen F. Glucose sensing and the mitochondrial alternative pathway are involved in the regulation of astaxanthin biosynthesis in the dark-grown Chlorella zofingiensis (Chlorophyceae). Planta (2008) 228:735–743.

Software evaluation - FlowJo

2008-09-10T08:48:00.008+01:00

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.

The European Cytometry Network webpage

2008-09-09T15:01:00.007+01:00

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.

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

2008-09-08T10:26:00.013+01:00

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:
Biotechnology
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.

Biosystematics
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.

Apomixis
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.

Endoreduplication:
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

2008-09-08T09:48:00.008+01:00

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

2008-09-08T09:04:00.008+01:00

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.

Xth Symposium of the International Organization of Plant Biosystematics

2008-06-23T16:20:00.008+01:00

The next Symposium of the International Organization of Plant Biosystematics will occur next week (from the 2nd to the 4th of July) in Visoké Tatry, Slovakia. This year the meeting will be devoted to the evolution of plants in montainous and alpine habitats. The impact that flow cytometry has been having in this area is well patent in the Symposium Scientific Programme as there will be one talk totally dedicated to it (Jan Suda, Praha - From individuals to populations: the impact of flow cytometry on understanding polyploid evolution in mountain plants) and some more talks that will certainly focus on data obtained using this powerful and high throughput technique.

The main topics that will be focused are:
PHYLOGEOGRAPHY
BIOGEOGRAPHY
EVOLUTIONARY PROCESSES IN EUROPEAN MOUNTAIN RANGES
POLYPLOIDY
MOLECULAR APPROACHES IN PLANT EVOLUTION
ECOLOGICAL FACTORS IN PLANT EVOLUTION
EVOLUTIONARY PROCESSES IN EXTRA-EUROPEAN MOUNTAINS
ROLE OF APOMIXIS IN PLANT EVOLUTION

There is still the possibility to register on site, so do not miss this opportunity to, besides enjoying a Symposium with a rather interesting programme (which should be the main purpose!), discover this beautiful mountain area of Slovakia.

I hope to see you there.

Plant Flow Cytometry - Far Beyond the Stone Age Commentary on Cytometry Journal

2008-06-19T10:11:00.003+01:00

In a close association with the review of Sergio Ochatt on the application of flow cytometry in plant breeding (see previous post) that appears in the current issue of Cytometry Part A journal we have been invited to write a commentary on the current state of flow cytometry in plant sciences. It is a short overview of the applications of flow cytometry to analyse plant cells and once again the blog, forum and FLOWer database were not forgotten. We hope that you enjoy the reading.

You can download it for free in here: Plant Flow Cytometry - Far Beyond the Stone Age

The first reference in a manuscript to the Plant FCM blog and forum

2008-06-18T15:51:00.004+01:00

In the last issue of Cytometry a review on the application of flow cytometry to plant breeding is presented by Sergio J. Ochatt from INRA (Dijon Cedex, France). The manuscript explores some of the interesting uses of flow cytometry in the area of plant breeding and, by the end, in an overview of the progress in recent years, both this blog and the plant flow cytometry forum are referred with the respective web address. We are very thankful for this mention and it is already a victory that we are slowly gaining some visibility within the plant FCM community.

Thank you all for being so supportive.

ISAC Congress - Plant FCM Workshop Presentations

2008-06-17T13:29:00.016+01:00

Despite that the Congress was already over almost one month ago, we are still summarizing some of the plant related events. Now, it is time to provide you with the presentations given in the plant FCM workshops (click on each image for download). The presentations may be used without copyright restrictions except for commercial or for profit use, provided there is some credit to the author and reference to this blog.

Workshop - Plant genome structure and gene expression - organized by David Galbraith and Jaroslav Dolezel

Presentations available by Jan Suda (Preparation and storage of plant samples for DNA flow cytometry), João Loureiro (The effect of cytosol on quantitative staining of nuclear DNA), Johann Greilhuber (Standardization and Standards), Jaroslav Dolezel (Chromosome analysis and sorting) and David Galbraith (Analysis of gene expression, including flow analysis and sorting of organelles and large cells)

Workshop - Plant evolutionary biology, biosystematics and ecology - organized by Brian Husband and Jan Suda

Presentations available by Jan Suda (The impact of FCM on plant Biosystematics and Taxonomy), Paul Kron (Flow Cytometry: Applications in the Study of Plant Reproductive Systems) and Brian Husband (Flow Cytometry and The Evolutionary Dynamics of Polyploids).

We hope that you enjoy the presentations.

Flow Cytometry Blog

2008-06-16T10:57:00.004+01:00

While surfing the net for some information about FCM courses I found this blog (link provided bellow) that lists some of the courses that will be lectured this year.

There are not Plant FCM-specific courses listed, but the basis of FCM is the same for all the fields of biology, so if you are interested in learning more about FCM, you should try some of the courses listed in that page, some are hands-on so you will get a lot of practical knowledge as well.

http://www.squidoo.com/flowcytometrycourses

Cheers

List of recently published papers on plant flow cytometry - May

2008-06-08T11:28:00.009+01:00

Below is the list of papers that came to our hands/knowledge during the month of April. In here there are already included some of the contributions made through the FLOWer database webpage. Many thanks for the authors that contributed with their work.

Genome size:
Carvalho CR, Clarindo WE, Praça MM, Araújo FS, Carels N. Genome size, base composition and karyotype of Jatropha curcas L., an important biofuel plant. Plant Science (2008) 174:613-617.

Rossi AAB, Clarindo WR, Carvalho CR, Oliveira LO. Karyotype and nuclear DNA content of Psychotria ipecacuanha: a medicinal species. Cytologia 73 (2008):53–60.

Ecology
Ayres DR, Grotkopp E, Zaremba K, Sloop CM, Blum MJ, Bailey JP, Anttila CK, Strong DR. Hybridization between invasive Spartina densiflora (Poaceae) and native S. foliosa in San Francisco Bay, California, USA. American Journal of Botany (2008) 95:713-719.

Biotechnology
Makowczynska J, Andrzejewska-Golec E, Sliwinska E. Nuclear DNA content in different plant materials of Plantago asiatica L. cultured in vitro. Plant Cell, Tissue and Organ Culture (2008) 94:65–71

Ploidy level:
Biotechnology
Kantartzi S, Roupakias DGProduction of aneuploids of the cotton hybrid G. barbadense x G. hirsutum L. via intergeneric pollination with Abelmoschus esculentus. Euphytica (2008) 161:319-327.

Orbovic V, Calovic M, Viloria Z, Nielsen B, Gmitter FG, Castle WS, Grosser JW. Analysis of genetic variability in various tissue culture-derived lemon plant populations using RAPD and flow cytometry. Euphytica (2008) 161:329-335.

Guillemin ML, Faugeron S, Destombe C, Viard F, Correa JA, Valero M. Genetic variation in wild and cultivated populations of the haploid-diploid red alga Gracilaria chilensis: how farming practices favor asexual reproduction and heterozygosity. Evolution (2008) 62-6: 1500–1519

Functional cytometry:
Apoptosis
Tilbrook J, Tyerman SD. Cell death in grape berries: varietal differences linked to xylem pressure and berry weight loss. Functional Plant Biology (2008) 35:173-184.

FLOWer database version 1.0 has just been launched

2008-06-02T15:47:00.007+01:00

I am very pleased to announce that version 1.0 of the FLOWer database is finally ready and online (http://flower.web.ua.pt/). After some serious problems with the programming of the previous version of the database, we are very glad that the first release of the database is up and running. You are welcome to visit it and I encourage you to use the database as a unique resource of publications on DNA flow cytometry in plant sciences. Your opinion is very important to us, so it would be nice to receive any feedback through the shoutbox available in the home page or directly to this e-mail. The database presently harbours 826 publications, and you are welcome to provide us with any missing ones through the contribution area available in the menu bar of the home page.

This is part of the e-mail that was sent to many colleagues of the plant flow cytometry area, where this blog and the forum of plant flow cytometry were also promoted. I hope that you like all these resources that were made available to you.

Many thanks for stopping by.

The "naughty" orchid

2008-06-02T15:10:00.008+01:00

I know that it is somehow offtopic, but I couldn't resist... A. Gaskett and co-workers have just discovered that sexually deceptive orchids from genus Cryptostylis, when mimicking female insects, frequently lead to pollinators ejaculation and waste of sperm. The consequences of such "naughty" behaviour are discussed in detail by the authors. Worth reading!

Abstract: Sexually deceptive orchids lure pollinators by mimicking female insects. Male insects fooled into gripping or copulating with orchids unwittingly transfer the pollinia. The effect of deception on pollinators has been considered negligible, but we show that pollinators may suffer considerable costs. Insects pollinating Australian tongue orchids (Cryptostylis species) frequently ejaculate and waste copious sperm. The costs of sperm wastage could select for pollinator avoidance of orchids, thereby driving and maintaining sexual deception via antagonistic coevolution or an arms race between pollinator learning and escalating orchid mimicry. However, we also show that orchid species provoking such extreme pollinator behavior have the highest pollination success. How can deception persist, given the costs to pollinators? Sexually-deceptive-orchid pollinators are almost exclusively solitary and haplodiploid species. Therefore, female insects deprived of matings by orchid deception could still produce male offspring, which may even enhance orchid pollination.

The access to the full article can be found here.

Some other ISAC posters related with plant flow cytometry

2008-06-02T12:51:00.012+01:00

After having talked with some of the participants related with plant flow cytometry, some of them agreed in sending me a jpg version of their posters. Please click on each image for the full size of the poster. As soon as I receive more posters, I will update this post.

Contributors:
Tomas Urfus - Department of Botany, Charles University in Prague, Czech Republic.
Sara V. Petersson - Umea Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea, Sweden.
Jingly Zhang - HortResearch, New Zealand.

Many thanks to all the contributors.

First review to the book Flow Cytometry with Plant Cells

2008-05-27T08:51:00.008+01:00

The last issue of Cytometry part A (Volume 73A Issue 6) has just published the first review to the book Flow Cytometry with Plant Cells: Analysis of Genes, Chromosomes and Genomes that was launched last year (see the side bar for full details). The review was made by Dr. Sergio Ochatt from the INRA, Dijon, France and the author carefully summarized what the book has to offer.You can download it for free by clicking this link.

As an author of one chapter I am very happy to finally see a review to the book. I am positive that it will be a good promotion to the book, helping it to reach an even broader number of researchers.

Just one final remark: on the review there is an error on the link to the FLOWer database. The correct link is: http://flower.web.ua.pt/.

ISAC Congress - The plant sciences team

2008-05-25T14:45:00.004+01:00

For prosperity the picture of the organizing team of the plant sciences sections of the ISAC Congress.

(from left to right: Jaroslav Dolezel, João Loureiro, David Galbraith, Jan Suda, Johann Greilhuber, Brian Husband and Paul Kron)

ISAC Congress - Day 5

2008-05-25T14:03:00.010+01:00

And so the last day of the XXIV ISAC Congress came, and since the morning we could see the difference in the number of participants that were present in the Budapest Sportsarena. After 4 long days, the exhaustion was already felt, personally speaking, but there was still time for some last chatting with the commercial exhibiters and most importantly, to profit from another interesting workshop dedicated to the plant sciences. Jan Suda, Brian Husband and Paul Kron brought for the first time the world of plant evolutionary biology, biosystematics and ecology to the ISAC Congress, and I was very happy to witness that at least a dozen participants were interested. As expected, the workshop was very good with the speakers presenting several examples on the potentialities that flow cytometry has on such fields together with some "controversy" related topics on best practices.

Then was time to relax, drink some hungarian beers in a local pub and eat some typical food, before going to rest with the idea that everything was done to fulfil the objectives of the Congress. Of course, we leave the evaluation for the participants... and we hope that they have enjoyed as much as I did.

ISAC Congress - Day 4

2008-05-21T13:16:00.007+01:00

The Day 4 of the now International Society of Advancements on Cytometry saw the comeback of the plant sciences, first by the presence of Jaroslav Dolezel in the Parallel Session of "High Throughput, High Content Analysis" with the very interesting talk on "Development of Flow-Based Strategies for Genomics of Crop Plants". There were also some interesting talks on the Advances in Flow Cytometry Instrumentation, especially those related with Acoustically Focused Sample Streams.

The day continued with the presentation of the FlowJo Software, this time dedicated to the bare basics. It seems quite a powerful tool, but still I would like to test it myself to evaluate which features may be of particular interest for plant DNA flow cytometry purposes. Again, and as with the new instruments, I will soon dedicate a post to the new software that was presented in the Congress.

In the afternoon the first Workshop dedicated to plants took place "Plant Genome Structure and Gene Expression", and to our surprise up to 25 people were present, which clearly surpassed our best expectations. The Workshop was wonderfully conducted by Jaroslav Dolezel and David Galbraith, and we had nice talks made by Jan Suda, Johann Greilhuber and by both chairmans, which covered several topics on the application of FCM in plant sciences, from sample preparation and storage, standards and standardizations, chromosome sorting for studies of genome structure and protoplasts and nuclei sorting for studies of gene expression. I had the opportunity to present some slides on the effect of cytosol on the quantitative staining of DNA, which despite being well received, w perhaps too technical for what was intended. However in each talk, some interesting questions were made and in the end we were satisfied with the overall output and reception of the workshop.

The poster session was just afterwards and again it was a nice opportunity to present the FLOWer database to many different people. The reception was good and it was a very nice idea of the congress organizers to put all the poster of similar areas close to each other.

By the end of the day, I was almost "dead" but there were still some forces for some good dinner and fruitful discussions.

ISAC Congress - Day 3

2008-05-21T12:57:00.004+01:00

The ISAC continues and the Day 3 was for me mostly dedicated to the commercial exhibitors. The Exhibit Hall presents many interesting offers and we can see the rise of smaller companies that are providing very interesting and competitive instruments. From what concerns the plant flow cytometry world, where the Partec flow cytometers rule, tough competition may start to appear. Partec itself presented their latest offers in the lunch commercial tutorial, but later on, in a different post, I will make a more dedicate overview of which (new) instruments were presented in the congress that might be of interest to plant flow cytometrists. The Congress itself was not very attractive, i.e., after the extraordinary Sunday it came the more so... so Monday...

Some more ISAC photos

2008-05-19T15:43:00.007+01:00

The Budapest Sportsarena, home of the ISAC Congress for 5 days:

The exhibit hall:

The main auditorium:

ISAC Congress - Day 2

2008-05-19T15:22:00.005+01:00

The second day of the ISAC congress may well be remembered as one of the most interesting, despite three days are still to come.

The day couldn't have started better with the interesting parallel session on the "Advances in Flow Cytometry Instrumentation I" where I would like to highlight the innovative approach directed to increase the measurement rates of current flow cytometers, laser rastering. The session was pretty full has it can be easily perceived from the picture.

Further highlights from Sunday include the impact that cytometry has been having in Marine Microbiology, as impressively presented by Ger van der Engh, and the High-Throughput microscopy analysis of the cytoskeleton, showed by Ronald Vale.

The commercial tutorial given by Tree Star, Inc. on the FlowJo software and on what advanced features will be present in the upcoming versions of the software was also quite interesting.

However, the cherry on top of the cake (I hope that this expression also makes some sense in English) was Howard Shapiro talk by the end of the day. As usual, he guided us through the History of Cytometry with his nice, sometimes bitter, sense of humour that pleased all the audience. For the end, a new version of his famous poem, now renamed as "There Is A Business Like Flow Business", was presented, wonderfully accompanied by background music and his still nice voice.

Our poster on the FLOWer database presented in ISAC Congress 2008

2008-05-17T15:58:00.003+01:00

ISAC Congress - Day 1

2008-05-17T15:38:00.010+01:00

Today, the XXIV International Congress of ISAC started in the beautiful city of Budapest. As promoted in previous posts of the blog, right in early morning the first activity related to plant flow cytometry, the tutorial dedicated to the estimation of genome size in plants, took place. Due to the extra costs of such an activity together with the already high costs of the Congress, only two participants attended to the tutorial. So, it was one of those occasions where the tutors outnumbered the students/participants... what a luxury! More seriously, we were sorry that there were not more people interested in our area, but I must also say that our expectations were not so high, as most of the participants are from the biomedical field. In case you are interested in knowing what you've missed, you can download the presentation in pdf format at: http://rapidshare.com/files/115567579/Tutorial__final_.pdf.html

The poster that we bring to the congress is already mounted in its panel just near the entrance of the main room of the Arena, where the chaos still rules with all the commercial exhibitors preparing their booth's with their top products.

The Congress officially started in the afternoon with the Frontiers talks dedicated to some technological advances in cytometry and with the Keynote Lecture given by Dr. Lansing Taylor on the Evolution of Image Cytometry.

Now, it is time for the Opening Reception, a nice opportunity to meet other researchers while snacking and drinking some "traditional" Hungarian starters.

The ISAC congress is coming...

2008-05-05T16:24:00.009+01:00

The XXIV International Congress of ISAC is starting already in the following 17th of May and I look forward for the event. I will make a daily report of the congress, accompanied by some documenting pictures. So keep tuned...

For your appetizing I will leave you with the advertising that will be made of one of the highlights in what concerns plant flow cytometry - the Workshop "Plant Genome Structure and Gene Expression". I hope that all the people in the picture are heading to the Budapest Sportsarena for the workshop. We do not mind the sporty clothes!

Dear ISAC Congress Attendee:

Jaroslav Dolezel and David Galbraith would like to invite you to attend Workshop 5 “Plant Genome Structure and Gene Expression” at the International ISAC Congress in Budapest. This workshop is scheduled for 15:45-17:15 on Tuesday, 20 May 2008, and will be held in the Red Room.

This workshop is aimed not simply at scientists interested in employing flow and image cytometry for the manipulation of plant cells, tissues, organs, and organelles. It also will provide valuable information for Operators and Core Managers having no prior experience with plant samples, who increasingly will encounter plant scientists interested in using their technologies and instruments in their plant-based research.

Topics to be presented and discussed will include:

Preparation and storage of samples for DNA flow cytometry.
Combating the negative effect of cytosol on nuclear DNA staining.
Standardization for reliable estimation of nuclear genome size.
Chromosome isolation and sorting.
Analysis of gene expression, including flow analysis and sorting of organelles and large cells.

There will also be opportunities provided for questions, comments, etc., from the audience.

WORKSHOP PROGRAM:

Moderators: Jaroslav Dolezel (Olomouc, CR) and David Galbraith (Tucson, USA)

Short presentations on each topic will be given by:

Jan Suda (Charles University in Prague, Czech Republic)
Johann Greilhuber (University of Vienna, Austria)
João Loureiro (Charles University in Prague, Czech Republic)
Jaroslav Dolezel (Institute of Experimental Botany, Olomouc, Czech Republic)
David Galbraith (University of Arizona, Tucson, USA)

Open Discussion will follow.

ISAC XXIV International Congress, May 17-21, 2008, Budapest, Hungary
http://www.isac-net.org/congress2008/

List of recently published papers on plant flow cytometry - April

2008-05-05T14:46:00.010+01:00

As a usual section of our blog, you can find below the list of papers that came to our hands/knowledge during the month of April.

Genome size:
Nucleotypic effect
Francis D, Davies MS, Barlow PW. A strong nucleotypic effect on the cell cycle regardless of ploidy level. Annals of Botany (2008) 101:747-757.

Ecology
Sweigart AL, Martin NH, Willis JH. Patterns of nucleotide variation and reproductive isolation between a Mimulus allotetraploid and its progenitor species. Molecular Ecology (2008) 17:2089-2100.

Ploidy level:
Biotechnology
Ochatt SJ, Sangwan RS. In vitro shortening of generation time in Arabidopsis thaliana. Plant Cell, Tissue and Organ Culture (2008) 93:133-137.

Zale J, Ohnoutkova L, West D, Sams C, Biggerstaff J, Le Pull M. Micropropagation of field-grown perennial teosinte from node culture. Crop Science (2008) 48:651-655.

Soriano M, Cistue L, Castillo AM. Enhanced induction of microspore embryogenesis after n-butanol treatment in wheat (Triticum aestivum L.) anther culture. Plant Cell Reports (2008) 27:805-811.

Leskovsek L, Jakse M, Bohanec B. Doubled haploid production in rocket (Eruca sativa Mill.) through isolated microspore culture. Plant Cell, Tissue and Organ Culture (2008) 93:181-189.

Biosystematics
Arndt S. Novelties in the Festuca valesiaca group (Poaceae) from the central Alps. Plant Systematics and Evolution (2008) 271:129-142.

Toxicology
Bakos F, Darkó E, Gáspár L, Ambrus H, Barnabás B. A cytological study on aluminium-treated wheat anther cultures resulting in plants with increased Al tolerance. Plant breeding (2008) 127:235-240.

Recent requests for help

2008-04-23T12:30:00.006+01:00

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: alfonso.blanco@ucd.ie)
Flow Cytometry Core Facilities
UCD - Conway Institute of Biomolecular & Biomedical Research
University College Dublin,
IRELAND"

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..

Thanks,

Roman Navratil , Ph.D. (e-mail: Roman.Navratil@i-cyt.com)
Applications Specialist
iCyt Mission Technology, Inc.
Praha, CZECH REPUBLIC"

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.

The Annals of Botany Plant Genome Horizons Special Issue

2008-04-16T13:42:00.011+01:00

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.

Contribution area of the FLOWer database is available

2008-04-13T12:09:00.006+01:00

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

2008-04-13T11:19:00.011+01:00

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
Germany

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

Oxalis genus in South Africa

2008-04-09T07:47:00.004+01:00

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.

Update of the FLOWer database

2008-04-07T19:33:00.008+01:00

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.

Late-breaking submissions on ISAC 2008 congress

2008-04-03T17:05:00.005+01:00

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!

FESPB CONGRESS 2008

2008-04-01T16:25:00.006+01:00

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: http://www.fespb2008.org/outline.htm
and the event homepage: http://www.fespb2008.org/

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

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

2008-04-01T16:05:00.007+01:00

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

2008-04-01T09:06:00.013+01:00

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

2008-03-06T15:28:00.010Z

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

2008-03-06T14:34:00.002Z

The European Cytometry Network Meeting - 2.0 Cytometry

2008-03-05T14:20:00.010Z

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

2008-03-05T13:17:00.009Z

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

2008-03-04T15:31:00.005Z

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

View Larger Map

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.

Forum members location

2008-03-04T14:20:00.003Z

The forum of plant flow cytometry has been quite inactive in the recent times, despite that a recent post by Alaa Cradock has been published recently. We are thinking on some strategies to promote it adequately.

For the moment, here is the map of the current forum members. I am happy that we have members of many different origins.

View Larger Map

Beer consumption vs. scientific performance

2008-02-19T14:40:00.005Z

Yes, it is true, someone made it, and the results are according to my predictions surprising. Tomás Grim from the Department of Zoology of Palacký University in Olomouc (Czech Republic) correlated the consumption of alcohol, particularly beer, with the publication output, using the "ecologists of Czech Republic" as the study group. And he was able to publish it in a renowned journal of ecology (Oikos).

So, the results showed that an increasing beer consumption per capita is associated with lower numbers of papers, total citations, and citations per paper. Not to talk, with an increase of "belly" diameter (data not shown in the paper).

Below follows the abstract and the link for the full text (if available from Blackwell Publishing):

Publication output is the standard by which scientific productivity is evaluated. Despite a plethora of papers on the issue of publication and citation biases, no study has so far considered a possible effect of social activities on publication output. One of the most frequent social activities in the world is drinking alcohol. In Europe, most alcohol is consumed as beer and, based on well known negative effects of alcohol consumption on cognitive performance, I predicted negative correlations between beer consumption and several measures of scientific performance. Using a survey from the Czech Republic, that has the highest per capita beer consumption rate in the world, I show that increasing per capita beer consumption is associated with lower numbers of papers, total citations, and citations per paper (a surrogate measure of paper quality). In addition I found the same predicted trends in comparison of two separate geographic areas within the Czech Republic that are also known to differ in beer consumption rates. These correlations are consistent with the possibility that leisure time social activities might influence the quality and quantity of scientific work and may be potential sources of publication and citation biases.

Link

Enjoy your reading!

Annals of Botany - Plant Genome Horizons - Forthcoming Special Issue

2008-02-01T09:59:00.000Z

The Annals of Botany, one of the leading journals in plant genome publications, is preparing another special issue, entitled "Plant Genome Horizons". This special issue will contain some of the works that were presented in the occasion of the conference with the same name (Kew, 16 and 17th of April 2007) that marked Prof. Mike Bennett's retirement and celebrated his scientific career.

From the Annals of Botany future papers here follows some of the articles that will be included in this forthcoming issue. Please note that some of them are already available online via the AoBPreview

A Century of B Chromosomes in Plants ? So What?
Jones RN, Viegas W, Houben A

Dissecting Meiosis of Rye using Translational Proteomics
Phillips D, Mikhailova EI, Timofejeva L, Mitchell JL, Osina O, Sosnikhina SP, Jones RN, Jenkins G

Cytochemistry and C-values: The Less-well Known World of Nuclear DNA Amounts
Greilhuber J

Detailed Dissection of the Chromosomal Region Containing the Ph1 Locus in Wheat Triticum aestivum: With Deletion Mutants and Expression Profiling
Al-Kaff N, Knight E, Bertin I, Foote T, Hart N, Griffiths S, Moore G

Biosystematics and Conservation: A Case Study with Two Enigmatic and Uncommon Species of Crassula from New Zealand
De Lange PJ, Heenan PB, Keeling DJ, Murray BG, Smissen R, Sykes WR

Anthocyanin Inhibits Propidium Iodide DNA Fluorescence in Euphorbia pulcherrima: Implications for Genome Size Variation and Flow Cytometry
Bennett MD, Price HJ, Johnston, JS

Review. Genome Size Scaling through Phenotype Space
Knight CA, Beaulieu JM

The Ups and Downs of Genome Size Evolution in Polyploid Species of Nicotiana (Solanaceae)
Leitch IJ, Hanson L, Lim KY, Kovarik A, Chase MW, Clarkson JJ, Leitch AR

Review: Allopolyploidization Accommodated Genomic Sequence Changes in Triticale
Ma X-F, Gustafson JP

When Genomes Collide: Aberrant Seed Development Following Maize Interploidy Crosses
Pennington PD, Costa LM, Gutierrez-Marcos JF, Greenland AJ, Dickinson HG

Development of a Genomic Microsatellite Library in Perennial Ryegrass (Lolium perenne) and its Use in Trait Mapping
King J, Thorogood D, Edwards KJ, Armstead IP, Roberts L, Skøt K, Hanley Z, King IP

Evolution of rDNA in Nicotiana Allopolyploids: A Potential Link between rDNA Homogenization and Epigenetics
Kovarik A, Dadejova M, Lim YK, Chase MW, Clarkson JJ, Knapp S, Leitch AR

We look forward for this Special Issue of AoB as the manuscripts that will be included seem very promising.

List of recently published papers on plant flow cytometry - December and January

2008-02-01T08:34:00.000Z

This month exceptionally we will post the recently published papers of the last two months, December and January.

Review:
Knight CA, Beaulieu JM. Genome size scaling through phenotype space. Annals of Botany (online)

Genome size:

Leitch IJ, Hanson L, Lim KY, Kovarik A, Chase MW, Clarkson JJ, Leitch AR. The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae). Annals of Botany (online)

Smarda P, Bures P, Horová L, Foggi B, Rossi G. Genome size and GC content evolution of Festuca: ancestral expansion and subsequent reduction. Annals of Botany (2008) 101:421-433

Ploidy level:
Kubátová B, Trávnícek P, Bastlová D, Curn V, Jarolímová V, Suda J. DNA ploidy-level variation in native and invasive populations of Lythrum salicaria at a large geographical scale. Journal of Biogeography 35:167-176

Halverson K, Heard SB, Nason JD, Stireman JO, III. Origins, distribution, and local co-occurrence of polyploid cytotypes in Solidago altissima (Asteraceae). American Journal of Botany (2008) 95:50-58

Clarindo WR, de Carvalho CR, Araújo FS, Abreu IS, Otoni WC. Recovering polyploid papaya in vitro regenerants as screened by flow cytometry. Plant Cell, Tissue and Organ Culture (2008) 92:207-214

Shi Y, Xu G, Warrington TB, Murdoch GK, Kazala EC, Snyder CL, Weselake RJ. Microspore-derived cell suspension cultures of oilseed rape as a system for studying gene expression. Plant Cell, Tissue and Organ Culture (2008) 92:131-139

Nimura M, Kato J, Mii M, Ohishi K. Cross-compatibility and the polyploidy of progenies in reciprocal backcrosses between diploid carnation (Dianthus caryophyllus L.) and its amphidiploid with Dianthus japonicus Thunb. Scientia Horticulturae (2008) 115:183-189

Technical article - cytosolic compounds:
Bennett M, Price HJ, Johnston JS. Anthocyanin inhibits propidium iodide DNA Fluorescence in Euphorbia pulcherrima: implications for genome size variation and flow cytometry. Annals of Botany (online)

If you fell that there are some papers missing (e.g., your papers), please send an e-mail to jloureiro@ua.pt or leave a comment on this post.

An update on the European Cytometry Network Meeting

2008-01-22T16:04:00.000Z

As posted below, with the aim to create a network of European Cytometrists, next 28th and 29th of February a meeting will be held in Heidelberg, Germany. Now, there are more details concerning the meeting, particularly, the preliminary programme and the registration procedure (by the way, the deadline for registration was extended until the 3rd of February). Head to the meeting webpage at the EMBL facility for this and more information.

New year, new life

2008-01-22T15:30:00.001Z

Dear colleagues,

This new year brought me an almost new life, as I am since last week connected with the Department of Botany of the Charles University in Prague (Czech Republic) and with the Laboratory of Flow Cytometry of the Institute of Botany in Pruhonice, where I will continue my studies (Post-Doc). I left many nice friends and colleagues in the Department of Biology of the University of Aveiro (Portugal) but it was time to move on, and the Czech Republic, especially the group of Jan Suda, is the best place to progress with my scientific career.

I am really excited with this new phase, but I am still adapting to the nice Czech culture, especially to its difficult language and cold temperatures, and to different flow cytometers.

I will try to keep the blog updated, and new ideas for it are welcome. Please post them in the comments to this post.

The best wishes for 2008.

João Loureiro

List of recently published papers on plant flow cytometry - November

2007-12-14T11:41:00.000Z

Genome size:

Błocka-Wandas M, Sliwinska E, Grabowska-Joachimiak A, Musial K, Joachimiak AJ. Male gametophyte development and two different DNA classes of pollen grains in Rumex acetosa L., a plant with an XX/XY₁Y₂ sex chromosome system and a female-biased sex ratio. Sexual Plant Reproduction (2007) 20:171-180

Simonovik B, Ivancic A, Jakse J, Bohanec B. Production and genetic evaluation of interspecific hybrids within the genus Sambucus. Plant Breeding (2007) 126:628-633

Besnard G, Garcia-Verdugo C, Rubio De Casas R, Treier UA, Galland N, Vargas P. Polyploidy in the Olive complex (Olea europaea): evidence from flow cytometry and nuclear microsatellite analyses. Annals of Botany (2008) 101: 25-30

Siljak-Yakovlev S, Stevanovic V, Tomasevic M, Brown SC, Stevanovic B. Genome size variation and polyploidy in the resurrection plant genus Ramonda: Cytogeography of living fossils. Environmental and Experimental Botany (2008) 62:101–112

Ploidy level:
Schönswetter P, Lachmayer M, Lettner C, Prehsler D, Rechnitzer S, Reich DS, Sonnleitner M, Wagner I, Hülber K, Schneeweiss GM, Trávnícek P, Suda J. Sympatric diploid and hexaploid cytotypes of Senecio carniolicus (Asteraceae) in the Eastern Alps are separated along an altitudinal gradient. Journal of Plant Research (2007) 120:721-725

Tiébré MS, Bizoux JP, Hardy OJ, Bailey JP, Mahy G. Hybridization and morphogenetic variation in the invasive alien Fallopia (Polygonaceae) complex in Belgium. American Journal of Botany (2007) 94:1900–1910

Okada T, Catanach AS, Johnson SD, Bicknell RA, Koltunow AM. An Hieracium mutant, loss of apomeiosis 1 ( loa1 ) is defective in the initiation of apomixis. Sexual Plant Reproduction (2007) 20:199-211

Abel S, Becker HC. The effect of autopolyploidy on biomass production in homozygous lines of Brassica rapa and Brassica oleracea. Plant Breeding (2007) 126:642-643

Sheng X, Liu F, Zhu Y, Zhao H, Zhang L, Chen B. Production and analysis of intergeneric somatic hybrids between Brassica oleracea and Matthiola incana. Plant Cell, Tissue and Organ Culture (2008) 92:55-62

Kao RH. Origins and widespread distribution of co-existing polyploids in Arnica cordifolia (Asteraceae). Annals of Botany (2008) 101:145–152

Mráz P, Singliarová B, Urfus T, Krahulec F. Cytogeography of Pilosella officinarum (Compositae): altitudinal and longitudinal differences in ploidy level distribution in the Czech Republic and Slovakia and the general pattern in Europe. Annals of Botany (2008) 101:59-71

European Cytometry Network meeting

2007-12-10T19:57:00.000Z

Last October during the DGfZ meeting, the Flow Cytometry Core Laboratory at EMBL Heidelberg has proposed to form an European network of Cytometrists with the aim of close co-operation between different cytometry Societies, Organisations and Laboratories within Europe. More specifically the goals of these network will focus on education, on the promotion of cytometry techniques and on the support of local and regional meetings. You can have a look at the poster that was presented in the DGfZ meeting in here.

For discussing such a network the FCC Laboratory is organizing a meeting to take place at EMBL Heidelberg, Germany on the 28th and 29th of February 2008. Please head to their webpage for more details.

We have just been invited by Andy Riddell to present a talk about plant flow cytometry in the meeting, which is quite an honour for us. As soon as we have more details we will give further news in the blog and forum.

A special acknowledgement to Andy Riddell for all his efforts.

ISAC - XXIV International Congress

2007-11-15T11:45:00.000Z

The next congress of ISAC - International Society for Analytical Cytology will be held next May (17th to 21st) in Budapest. It is with great pleasure that we announce that a tutorial session and two workshops focused on plant flow cytometry were approved for presentation.

Scientific tutorial: Estimation of genome size in plants using flow cytometry
Tutors: Jan Suda, João Loureiro and Johann Greilhuber
Abstract: The last two decades have seen a significant increase in the use of flow cytometry for estimation of genome size in plants (either in absolute terms or in relative units, as an indicator of ploidy level), with the data being successfully utilized in various fields of plant sciences, including biosystematics, ecology, evolutionary biology and biotechnology. This tutorial will focus primarily on the biological significance of genome size variation in plants and on the methodological approaches used to analyse the nuclear DNA content of cells. A set of best practice rules will be presented, and special attention will be given to the strategies that may be employed to investigate recalcitrant plant material. The practical session will include basic protocols using several different isolation buffers and DNA-selective fluorochromes for staining intact plant nuclei. The effect of chemical additives (antioxidants, preservatives) on the quality of histograms will be demonstrated. The tutorial is aimed at newcomers in plant flow cytometry as well as at workers in other fields interested in learning more about specific features of plant material.

Workshop: The impact of flow cytometry on plant evolutionary biology, biosystematics and ecology
Organizers: Brian Husband and Jan Suda

Abstract: Since the 1980s, use of flow cytometry (FCM) in plant population and evolutionary biology, biosystematics, and ecology has expanded dramatically both in scope and frequency. With its ability to collect several quantitative parameters, simultaneously, for large numbers of particles, FCM is widening the diversity of attributes that can be explored on a population scale and the taxonomic, spatial, and temporal scope of these investigations. As a result, the technique has enabled large-scale comparative analyses of genome size evolution, taxonomic identification and delineation, and is advancing new research programs in polyploid evolution and reproductive biology. In combination with other methodological approaches, FCM promises qualitative advances in our understanding of genome multiplication and the population biology of vascular plants. Workshop facilitators will introduce some of the recent developments, problems and applications of FCM in plant population biology, biosystematics and evolution, and then lead a discussion on some or all topics. Two themes that will recur throughout these discussions are: (i) novel applications of flow cytometry as a result of the higher sample throughput and larger sample sizes possible compared to traditional methods; and (ii) the potential benefits of combining FCM with other, notably molecular, techniques.

Workshop: Plant genome structure and gene expression

Organizers: Jaroslav Dolezel and David Galbraith

Abstract: This 90 min workshop will comprise invited talks and talks selected from submitted abstracts. The talks will focus on the most advanced applications of flow cytometry in plants, with an emphasis on the analysis of plant genome structure and function. This includes, but is not restricted to, chromosome sorting for physical genome mapping and gene cloning, and global analysis of gene expression in specific cell types. This workshop is intended to attract a broad range of audience members, ranging from PhD students to senior researchers. To our knowledge, this will be the first scientific workshop at an international conference entirely devoted to advanced applications of flow cytometry in plants that focus on plant genome structure and function.

As soon as we know further details, we will update this post. So check regularly for updates.

New book - Protocols for Micropropagation of Woody Trees and Fruits

2007-11-12T13:03:00.000Z

A book on the micropropagation of woody trees and fruits has just been published by Springer Netherlands. Congratulations to the editors Mohan Jain S and Häggman H, for the nice collection of protocols. Flow cytometry was not forgotten and it was used in several protocols as an important tool to analyse the genetic fidelity of the obtained plants.

Below is the list of chapters where flow cytometry was employed:

S. Korban and I. Sul. Micropropagation of Coast Redwood (Sequoia sempervirens). pp. 23-32

C. Santos, J. Loureiro, T. Lopes and G. Pinto. Genetic Fidelity Analyses of In Vitro Propagated Cork Oak (Quercus suber L.). pp. 67-83

B. Pintos, J. Manzanera and M. Bueno. Protocol for Doubled-Haploid Micropropagation in Quercus suber L. and Assisted Verification. pp. 163-178

S. Murch, D. Ragone, W. Shi, A. Alan and P. Saxena. In vitro conservation and Micropropagation of Breadfruit (Artocarpus altilis, Moracea). pp. 279-288

M. Ostrolucká, A. Gajdošová, G. Libiaková, K. Hrubíková and M. Bežo. Protocol for Micropropagation of Selected Vaccinium spp. pp. 445-455

M. Ostrolucká, A. Gajdošová, G. Libiaková and E. Ondrušková. Protocol for Micropropagation of Vaccinium vitis-idaea L. pp. 457-464

J. Al-Khayri. Date Palm Phoenix dactylifera L. Micropropagation. pp. 509-526

List of recently published papers on plant flow cytometry - October

2007-11-12T08:36:00.000Z

After some silent period, we have decided to open a new monthly section where the recently published papers will be listed. This list corresponds to the manuscripts published on the month of October.

Reviews:
Kron P, Suda J, Husband BC. Applications of Flow Cytometry to Evolutionary and Population Biology. Annual Review of Ecology, Evolution, and Systematics 38 (online)

Greilhuber J. Cytochemistry and C-values: The Less-well-known World of Nuclear DNA Amounts. Annals of Botany (online) (From the forthcoming special issue Plant Genome Horizons).

Technical report:
Roberts AV. The use of bead beating to prepare suspensions of nuclei for flow cytometry from fresh leaves, herbarium leaves, petals and pollen. Cytometry (online).

Genome size:
Loureiro J, Kopecky D, Castro S, Santos C, Silveira P. Flow cytometric and cytogenetic analyses of Iberian Peninsula Festuca spp. Plant Systematics and Evolution (2007) 269:89–105

Suda J, Krahulcová A, Trávnícek P, Rosenbaumová R, Peckert T, Krahulec F. Genome Size Variation and Species Relationships in Hieracium Sub-genus Pilosella (Asteraceae) as Inferred by Flow Cytometry. Annals of Botany (2007) 100:1323–1335

Eilam T, Anikster Y, Millet E, Manisterski J, Sagi-Assif O, Feldman M. Genome size and genome evolution in diploid Triticeae species. Genome (2007) 50:1029-1037

Ploidy level:
Gillis K, Gielis J, Peeters H, Dhooghe E, Oprins J. Somatic embryogenesis from mature Bambusa balcooa Roxburgh as basis for mass production of elite forestry bamboos. Plant Cell, Tissue and Organ Culture (2007) 91:115–123

Bidani A, Nouri-Ellouz O, Lakhoua L, Sihachakr D, Cheniclet C, Mahjoub A, Drira N, Gargouri-Bouzid R. Interspecific potato somatic hybrids between Solanum berthaultii and Solanum tuberosum L. showed recombinant plastome and improved tolerance to salinity. Plant Cell, Tissue and Organ Culture (2007) 91:179–189

Soriano M, Cistué L, Vallés MP, Castillo AM. Effects of colchicine on anther and microspore culture of bread wheat (Triticum aestivum L.). Plant Cell, Tissue and Organ Culture (2007) 91:225–234

Fiuk A, Rybczynski JJ. The effect of several factors on somatic embryogenesis and plant regeneration in protoplast cultures of Gentiana kurroo (Royle). Plant Cell, Tissue and Organ Culture (2007) 91:263–271

Coelho CM, Wu S, Li Y, Hunter B, Dante RA, Cui Y, Wu R, Larkins BA. Identification of quantitative trait loci that affect endoreduplication in maize endosperm. Theoretical and Applied Genetics (2007) 115:1147–1162

Sharma SK, Bryan GJ, WinWeld MO, Millam S. Stability of potato (Solanum tuberosum L.) plants regenerated via somatic embryos, axillary bud proliferated shoots, microtubers and true potato seeds: a comparative phenotypic, cytogenetic and molecular assessment. Planta (2007) 226:1449–1458

Fras A, Juchimiuk J, Siwinska D, Maluszynska J. Cytological events in explants of Arabidopsis thaliana during early callogenesis. Plant Cell Rep (2007) 26:1933–1939

Allum JF, Bringloe DH, Roberts AV. Chromosome doubling in a Rosa rugosa Thunb. hybrid by exposure of in vitro nodes to oryzalin: the effects of node length, oryzalin concentration and exposure time. Plant Cell Reports (2007) 26:1977–1984

Fatta Del Bosco S, Siragusa M, Abbate L, Lucretti S, Tusa N. Production and characterization of new triploid seedless progenies for mandarin improvement. Scientia Horticulturae (2007) 114:258–262

Functional Plant FCM:
Yang J, Ma L, Zhang Y, Fang F, Li L. Flow cytometric identification of two diffeent rhodamine-123-stained mitochondrial populations in maize leaves. Protoplasma (2007) 231:249-252.

If there is any recent paper missing, please post its link in the comments that we will update this post accordingly. Once again, your contribution is very important.

The 2007 Ig Nobel Prize Winners

2007-10-12T10:36:00.000+01:00

For a little fun, below follows the list of the 2007 Ig Nobel Prizes awarded by the Improbable Research, whose lemma is: "For the achievements that first make people LAUGH then make them THINK".

Medicine: Brian Witcombe of Gloucester, UK, and Dan Meyer of Antioch, Tennessee, USA, for their penetrating medical report "Sword Swallowing and Its Side Effects."
Reference: "Sword Swallowing and Its Side Effects," Brian Witcombe and Dan Meyer, British Medical Journal, December 23, 2006, vol. 333, pp. 1285-7.

Physics: L. Mahadevan of Harvard University, USA, and Enrique Cerda Villablanca of Universidad de Santiago de Chile, for studying how sheets become wrinkled.
References: "Wrinkling of an Elastic Sheet Under Tension," E. Cerda, K. Ravi-Chandar, L. Mahadevan, Nature, vol. 419, October 10, 2002, pp. 579-80.
"Geometry and Physics of Wrinkling," E. Cerda and L. Mahadevan, Physical Review Letters, fol. 90, no. 7, February 21, 2003, pp. 074302/1-4.
"Elements of Draping," E. Cerda, L. Mahadevan and J. Passini, Proceedings of the National Academy of Sciences, vol. 101, no. 7, 2004, pp. 1806-10.

Biology: Prof. Dr. Johanna E.M.H. van Bronswijk of Eindhoven University of Technology, The Netherlands, for doing a census of all the mites, insects, spiders, pseudoscorpions, crustaceans, bacteria, algae, ferns and fungi with whom we share our beds each night.
References: "Autotrophic Organisms in Mattress Dust in the Netherlands," B. van de Lustgraaf, J.H.H.M. Klerkx, J.E.M.H. van Bronswijk, Acta Botanica Neerlandica, vol. 27, no. 2, 1978, pp 125-8.
"A Bed Ecosystem," J.E.M.H. van Bronswijk, Lecture Abstracts -- 1st Benelux Congress of Zoology, Leuven, November 4-5, 1994, p. 36.

Chemistry: Mayu Yamamoto of the International Medical Center of Japan, for developing a way to extract vanillin -- vanilla fragrance and flavoring -- from cow dung.
Reference: "Novel Production Method for Plant Polyphenol from Livestock Excrement Using Subcritical Water Reaction," Mayu Yamamoto, International Medical Center of Japan.

Linguistics: Juan Manuel Toro, Josep B. Trobalon and Núria Sebastián-Gallés, of Universitat de Barcelona, for showing that rats sometimes cannot tell the difference between a person speaking Japanese backwards and a person speaking Dutch backwards.
Reference: "Effects of Backward Speech and Speaker Variability in Language Discrimination by Rats," Juan M. Toro, Josep B. Trobalon and Núria Sebastián-Gallés, Journal of Experimental Psychology: Animal Behavior Processes, vol. 31, no. 1, January 2005, pp 95-100.

Literature: Glenda Browne of Blaxland, Blue Mountains, Australia, for her study of the word "the" -- and of the many ways it causes problems for anyone who tries to put things into alphabetical order.
Reference: "The Definite Article: Acknowledging 'The' in Index Entries," Glenda Browne, The Indexer, vol. 22, no. 3 April 2001, pp. 119-22.

Peace: The Air Force Wright Laboratory, Dayton, Ohio, USA, for instigating research & development on a chemical weapon -- the so-called "gay bomb" -- that will make enemy soldiers become sexually irresistible to each other.
Reference: "Harassing, Annoying, and 'Bad Guy' Identifying Chemicals," Wright Laboratory, WL/FIVR, Wright Patterson Air Force Base, Ohio, June 1, 1994.

Nutrition: Brian Wansink of Cornell University, for exploring the seemingly boundless appetites of human beings, by feeding them with a self-refilling, bottomless bowl of soup.
Reference: "Bottomless Bowls: Why Visual Cues of Portion Size May Influence Intake," Brian Wansink, James E. Painter and Jill North, Obesity Research, vol. 13, no. 1, January 2005, pp. 93-100.

Economics: Kuo Cheng Hsieh, of Taichung, Taiwan, for patenting a device, in the year 2001, that catches bank robbers by dropping a net over them.
Reference: U.S. patent #6,219,959, granted on April 24, 2001, for a "net trapping system for capturing a robber immediately."

Aviation: Patricia V. Agostino, Santiago A. Plano and Diego A. Golombek of Universidad Nacional de Quilmes, Argentina, for their discovery that Viagra aids jetlag recovery in hamsters.
Reference: "Sildenafil Accelerates Reentrainment of Circadian Rhythms After Advancing Light Schedules," Patricia V. Agostino, Santiago A. Plano and Diego A. Golombek, Proceedings of the National Academy of Sciences, vol. 104, no. 23, June 5 2007, pp. 9834-9.

Adapted from http://improbable.com/ig/ig-pastwinners.html#ig2007

New flow cytometry website

2007-10-02T16:11:00.000+01:00

The Flow Cytometry Core Facility of the European Molecular Biology Laboratory (EMBL) in Heidelberg has just launched a new interesting website with many downloadable resources, such as software, hardware designs, teaching tutorials and how-tos and educational resources (e.g., video tutorials).

It is certainly worth a look and as the developers of the website intend to regularly update it with new information and resources, one should return to read the latest contents.

The first week of the forum and blog

2007-10-01T14:19:00.001+01:00

Since the publicity of the forum a week and some days ago, we have received a nice feedback from the plant FCM community with 22 new members, totalling 26 members from diverse locations around the world (see figure).

More importantly, there has been some posting activity from some newly registered members. Below you can find the link to each of the topics started by the new members:
- Calibrating plant standards for flow cytometry (by alaacraddock);
- Substituting PVP (by pkron);
- DNA content using PI on FACScan (by georgina);
- The application of flow cytometry to count pollen grains (by scastro).

The questions that were posed are all very interesting, but members feedback/answer is still reduced.

Also, a new forum "Troublesome Plant Material" has been created and it is expected that members post the name of plant species which were impossible to analyse by FCM. Therefore, if other members had some previous experience with any of the posted species, some advice and solutions can be given.

This blog itself has received many visits, once again from the whole world (see image above). I hope that the blog is a nice complement to the forum and we promise to post any interesting news when appropriate. So please be aware of new posts and visit us regularly. Also, if you want you can comment any of the posts made so far. It is always nice to have some feedback from the readers.

The first days of the newly born...

2007-09-24T15:39:00.000+01:00

Dear colleagues,

Many thanks for your output in what concerns this blog and the forum on plant flow cytometry. Since the publicity made last Friday, we've seen a considerable increase of visits to the blog (please see the world map in the right column) and more than 10 new user registration's to the forum. I hope that both tools are of your interest.

So, the next phase to which I encourage you all, is to interact with both web platforms, i.e. to comment the posts of the blog (you can do this by clicking on the link below each post) and to post any interesting topics on the forum.

Also, I ask all of you if it is possible to forward the e-mail message of the post below, to the people of your list of contacts that may be interest on the topics covered in the blog and in the forum.

Finally, if you want to see a link to your laboratory webpage in the right column, please send me the details (i.e., name and head of laboratory, link), either by e-mail (jloureiro@ua.pt) or by posting them in the comments to this post.

The day zero

2007-09-21T22:03:00.000+01:00

May this be the day 0 of this Blog and of the Forum of Plant Flow Cytometry. Today I sent an e-mail to more than 390 corresponding authors of publications concerning plant flow cytometry and included in the FLOWer database, publicizing the blog and forum. Despite many of those e-mails came back with errors (possibly due to e-mail updates since appearance in publications), I believe that in many cases they arrived at the author's mailboxes with success. As a result, we've seen many visits to the blog and some registrations in the Forum, with the first non-jloureiro topic being posted. So, I must say that I am quite happy with the impact that the e-mail had today and I hope that it continues in the following days.

I encourage all of you to contribute either with comments to these posts or/and with topics in the forum. I also stimulate you to make as much publicity as possible, to see if we can gather a huge amount of researchers to this on-line community. Please remember that these new web resources will only work if you participate actively on them.

Below follows the e-mail that was sent today:

Dear colleagues,

It is with great pleasure that I announce the first forum and blog on plant flow cytometry. These two new platforms are at your disposal to discuss general topics in plant flow cytometry, to post any doubts or questions related to (the analysis of plant cells using flow cytometry) PLANT FLOW CYTOMETRY, to announce upcoming congresses and courses, etc.

Such platforms are only valuable if you participate actively and if there is a regular number of new posts and comments. Therefore, I invite you to register in the forum and use it on your best interests. The blog can be a very informal way of communicating and posting new and interesting information on plant flow cytometry, and you are encouraged to comment on the various topics that will be regularly posted.

You can access the forum at the following address: http://flowerdatabase.20.forumer.com/index.php and the blog at: http://flowerdatabase.blogspot.com/ .

These (two) new tools of communication appeared first as a companion to the FLOWER database (the Plant DNA Flow Cytometry Database: http://flower.web.ua.pt/), but are now directed to plant flow cytometry in general. Please consider that the FLOWER database is still in its beginning (beta version), and thus it still presents some flaws.

With best regards,

João Loureiro

New paper on Nature Protocols

2007-09-18T09:43:00.000+01:00

The Central Europe plant flow cytometry triangle team, i.e., Jaroslav Dolezel (Olomouc), Johann Greilhuber (Vienna) and Jan Suda (Prague), has just published another very interesting manuscript on the estimation of nuclear DNA content in plants using cytometry. This review and step-by-step protocol has just been published in Nature Protocols the online resource for protocols of the Nature Publishing Group.

The article is very carefully written and presents step-by-step protocols for the analysis of nuclear DNA content in plant tissues, with the underlining of the procedure's critical steps. A very useful troubleshooting table is also provided, with the possible reasons and solutions for the most common problems that may appear upon analysis of plant tissues using flow cytometry. Therefore the article is utterly recommended not only for beginners but also for more experienced users of the area of plant FCM.

Below follows the abstract and the link to the online version of the manuscript.

Abstract:
Flow cytometry (FCM) using DNA-selective fluorochromes is now the prevailing method for the measurement of nuclear DNA content in plants. Ease of sample preparation and high sample throughput make it generally better suited than other methods such as Feulgen densitometry to estimate genome size, level of generative polyploidy, nuclear replication state and endopolyploidy (polysomaty). Here we present four protocols for sample preparation (suspensions of intact cell nuclei) and describe the analysis of nuclear DNA amounts using FCM. We consider the chemicals and equipment necessary, the measurement process, data analysis, and describe the most frequent problems encountered with plant material such as the interference of secondary metabolites. The purpose and requirement of internal and external standardization are discussed. The importance of using a correct terminology for DNA amounts and genome size is underlined, and its basic principles are explained.

Author for correspondence: Jaroslav Dolezel; e-mail: dolezel@ueb.cas.cz

Online version

First diploid sequence for Homo sapiens

2007-09-07T09:28:00.000+01:00

At the turn of the millennium, the first reports of mapping the human genome—a data mosaic from numerous individuals—heralded an era of personalized medicine based on individual human genomes. But so far, the full genomic sequence from a single human being has not been formally published.

This has now come to reality with the publication of the first diploid genome sequence for Homo sapiens in PLoS Biology. The chosen one, or should I say fortunate one, was J. Craig Venter, the founder of the Institute for Genomic Research (TIGR) and considered one of the most influential people in the world list of Time magazine 2007.

An interactive and impressive poster of the sequenced genome is also made available by PLoS Biology. Be free to fly in to this nice animated flash poster.

Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. (2007). "The Diploid Genome Sequence of an Individual Human". PLoS Biology 5 (10).

Adapted from PLoS Biology

Welcoming

2007-09-06T15:46:00.000+01:00

Welcome to the Plant Flow Cytometry blog. This new way of communicating will be used to post any news concerning the application of flow cytometry to plant cells, with the FLOWer database getting particular attention. Other science news that deserve further attention will also be matter of our interests.