Late May 2009 papers

Some interest papers. I finally catch up.

A soil bacterium regulates plant acquisition of iron via deficiency-inducible mechanisms, Huiming Zhang, Yan Sun, Xitao Xie, Mi-Seong Kim, Scot E. Dowd, Paul W. Paré, Plant Journal 58(4):568-577.

Drought tolerance in Arabidopsis is controlled by the OCP3 disease resistance regulator, Vicente Ramírez, Alberto Coego, Ana López, Astrid Agorio, Víctor Flors, Pablo Vera, Plant Journal 58(4):578-591.

A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature, Bárbara Strasser, Mariano J. Alvarez, Andrea Califano, Pablo D. Cerdán, Plant Journal 58(4):629-640.

A genetic network of flowering-time genes in wheat leaves, in which an APETALA1/FRUITFULL-like gene, VRN1, is upstream of FLOWERING LOCUS T, Sanae Shimada, Taiichi Ogawa, Satoshi Kitagawa, Takayuki Suzuki, Chihiro Ikari, Naoki Shitsukawa, Tomoko Abe, Hiroyuki Kawahigashi, Rie Kikuchi, Hirokazu Handa, Koji Murai, Plant Journal 58(4):668-681.

Technology: The holy grail for plant biologists, Magdalena Skipper, Nature Reviews Genetics 10:350 (June 2009).
....Both studies rely on zinc-finger nucleases (ZFNs) — engineered enzymes that create double-stranded breaks at specific loci and that have previously been used to modify, in vitro, plant transgenes and endogenous genes in human cells.....

Precise genome modification in the crop species of Zea mays using zinc-finger nucleases, Shukla, V. K. et al., Nature 459:437-441.

High-frequency modification of plant genes using engineered zinc-finger nucleases, Townsend, J. A. & Wright, D. A. et al., Nature 459:442-445.

ARTICLE SERIES: Genome-wide association studies, Nature Reviews Genetics vol. 10 (June 2009).
In the past 2 years genome-wide association studies in humans have revealed dozens of disease-associated loci and have provided insights into the allelic architecture of complex traits. Along the way, much has been learned about how best to carry out such studies. The articles in this series examine these design issues and the technical challenges that remain; for example, identifying association signals and interpreting the molecular mechanisms by which they exert their biological functions.

ARTICLE SERIES: Genome-wide association studies: Detecting gene–gene interactions that underlie human diseases, Heather J Cordell, Nature Reviews Genetics 10, 392-404 (June 2009).

ARTICLE SERIES: Genome-wide association studies: Validating, augmenting and refining genome-wide association signals, John P. A. Ioannidis, Gilles Thomas & Mark J. Daly, Nature Reviews Genetics 10, 318-329 (May 2009).

Arabidopsis mutant deficient in 3 abscisic acid-activated protein kinases reveals critical roles in growth, reproduction, and stress, Hiroaki Fujii and Jian-Kang Zhu, PNAS 106(20):8380-8385.

Vernalization-induced flowering in cereals is associated with changes in histone methylation at the VERNALIZATION1 gene, Sandra N. Oliver, E. Jean Finnegan, Elizabeth S. Dennis, W. James Peacock, and Ben Trevaskis, PNAS 106(20):8386-8391.

The flowering hormone florigen functions as a general systemic regulator of growth and termination, Akiva Shalit, Alexander Rozman, Alexander Goldshmidt, John P. Alvarez, John L. Bowman, Yuval Eshed, and Eliezer Lifschitz, PNAS 106(20):8392-8397.

Plant biotechnology: Zinc fingers on target, Matthew H. Porteus, Nature 459, 337-338 (21 May 2009)
The existing methods of creating genetically modified plants are inefficient and imprecise. Zinc-finger technology offers the prospect of opening up a swifter and more exact route for crop improvement.
....The ability to create precise genetically modified plants is one approach to that end, and papers by Shukla et al.1 and Townsend et al.2 (pages 437 and 442 of this issue) provide a promising way forward. Both groups exploit the potential of enzymes called zinc-finger nucleases.

Plant cell biology: New receptors for ABA, Francesca Cesari, Nature Reviews Molecular Cell Biology 10:368-369 (June 2009).

The ubiquitin-26S proteasome system at the nexus of plant biology, Richard D. Vierstra, Nature Reviews Molecular Cell Biology 10:385-397 (June 2009).
The ubiquitin-26S proteasome system is one of the most pervasive pathways of intracellular protein regulation in plants. It controls hormone signalling, chromatin structure and transcription, tailoring morphogenesis, responses to environmental challenges, self-recognition and the battle between pathogens and their plant hosts.

Guidelines for Quantitative RT-PCR, Cathie Martin, Plant Cell 21:1023.

Deep Sequencing Maps the Maize Epigenomic Landscape, Nancy A. Eckardt, Plant Cell 21:1024-1026.

Real-Time Quantitative RT-PCR: Design, Calculations, and Statistics, Ivo Rieu and Stephen J. Powers, Plant Cell 21:1031-1033.

Web-Queryable Large-Scale Data Sets for Hypothesis Generation in Plant Biology, Siobhan M. Brady and Nicholas J. Provart, Plant Cell 21:1034-1051.

Stressed Out Over a Stress Hormone, Elizabeth Pennisi, Science 324(5930):1012 - 1013.
The hormone ABA lets plants handle rough times and holds promise for making drought-resistant crops, if only researchers could nail down its molecular partners.

Regulators of PP2C Phosphatase Activity Function as Abscisic Acid Sensors, Yue Ma, Izabela Szostkiewicz, Arthur Korte, Danièle Moes, Yi Yang, Alexander Christmann, and Erwin Grill, Science 324 (5930):1064.

Abscisic Acid Inhibits Type 2C Protein Phosphatases via the PYR/PYL Family of START Proteins, Sang-Youl Park, Pauline Fung, et al., Science 324 (5930):1068.

Turning a plant tissue into a living cell froth through isotropic growth, Francis Corson, Olivier Hamant, Steffen Bohn, Jan Traas, Arezki Boudaoud, and Yves Couder, PNAS 106(21):8453-8458.

Altered interactions within FY/AtCPSF complexes required for Arabidopsis FCA-mediated chromatin silencing, David Manzano, Sebastian Marquardt, Alexandra M. E. Jones, Isabel Bäurle, Fuquan Liu, and Caroline Dean, PNAS 106(21):8772-8777.

Rice OPEN BEAK is a negative regulator of class 1 knox genes and a positive regulator of class B floral homeotic gene, Ayako Horigome, Nobuhiro Nagasawa, Kyoko Ikeda, Momoyo Ito, Jun-Ichi Itoh, Yasuo Nagato, The Plant Journal 58(5):724 - 736.

Atmospheric chemistry: The man who smells forests, Erik Vance, Nature 459, 498-499 (2009).
Chemist Allen Goldstein has spent his career tracking elusive compounds emitted by trees. Erik Vance joined him for a tour of the woods.
... At sunrise, the trees start pumping out a complex mix of volatile organic compounds (VOCs), such as pine-scented terpenes. By mid-morning, the westerly breeze adds a dose of the VOC isoprene from oak woodlands about 30 kilometres away. Then, as the sun reaches its peak in the sky, pollution from California's Central Valley makes its way up into the mountains...
... Estimates suggest that the vast majority, perhaps up to 90%, of Earth's VOC output comes from vegetation ...

"Agriculture" Is Not a Dirty Word, Allen S. Levine, Science 324(5931):1140.
Agricultural science is ripe for a renaissance. For too many years, the agriculture sciences have been disparaged in the science and education communities, perhaps because agronomy, soil science, plant pathology, and animal science use a problem-solving approach rather than simply seeking knowledge.

PROFILE: RUTH LEY: Gut Reactions, Elizabeth Pennisi, Science 324(5931):1136 - 1137.
A young microbial ecologist is helping to transform medical microbiology into a modern interdisciplinary science.