List of recently published papers on plant flow cytometry - November

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

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

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

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

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

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

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

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...

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

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

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

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

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.