ISAC Congress - Day 4

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.

The Annals of Botany Plant Genome Horizons Special Issue

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

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

It is definitely worth reading.

Annals of Botany - Plant Genome Horizons - Forthcoming Special Issue

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.

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.

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