The comeback

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

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

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

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

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

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, organogenesis and pattern formation depend on formative divisions to specify and maintain pools of stem cells. In higher plants, these activities are essential to shape the final root architecture because the functioning of root apical meristems and the de novo formation of lateral roots entirely rely on it. We used transcript profiling on sorted pericycle cells undergoing lateral root initiation to identify the receptor-like kinase ACR4 of Arabidopsis as a key factor both in promoting formative cell divisions in the pericycle and in constraining the number of these divisions once organogenesis has been started. In the root tip meristem, ACR4 shows a similar action by controlling cell proliferation activity in the columella cell lineage. Thus, ACR4 function reveals a common mechanism of formative cell division control in the main root tip meristem and during lateral root initiation.

Another great achievement of plant chromosome flow sorting

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.