Early Jan 2009 papers

Here is some interest papers.

Circadian Clock Proteins LHY and CCA1 Regulate SVP Protein Accumulation to
Control Flowering in Arabidopsis, Sumire Fujiwara, Atsushi Oda, Riichiro Yoshida, Kanae Niinuma, Kana Miyata, Yusuke Tomozoe, Takeomi Tajima, Mayu Nakagawa, Kounosuke Hayashi, George Coupland, and Tsuyoshi Mizoguchi, Plant Cell 20:2960-2971 (2008).
The authors show that LHY and CCA1 control flowering time in continuous light in a GIGANTEA-CONSTANS independent manner. This involves interactions with the clock gene ELF3 and two MADS box proteins, SHORT VEGETATIVE PHASE and FLOWERING LOCUS C, which together act to coordinate the circadian clock and flowering time in Arabidopsis.

Special Feature: Method of the Year: Method of the Year 2008, Nature Methods 6(1):1 (January 2009).
With its tremendous potential for understanding cellular biology now poised to become a reality, super-resolution fluorescence microscopy is our choice for Method of the Year.

Maturing interactions, Nature Methods 6(1):2 (January 2009).
The maturation of large-scale protein-protein interaction methodologies calls for improved methods to assess performance and data quality.

Targeted translational profiling, Nicole Rusk, Nature Methods 6(1):7 (January 2009).
Tagging ribosomes in a cell type–specific way allows the isolation of mRNAs that are being translated in these cells.

Quantitative mass spectrometry, Allison Doerr, Nature Methods 6(1):34 (January 2009).
Quantitative mass spectrometry–based proteomics is now being applied on a large scale to address interesting biological questions.

High-throughput screening: designer screens, Nathan Blow, ature Methods 6(1):105 - 108 (January 2009).
Some researchers say an eighty-year-old statistical method can make setting up and analyzing high-throughput screens and large-scale experiments faster and more efficient. So why are more biologists not flocking to use this tool?

CORAL REEFS: Calcification Rates Drop in Australian Reefs, Elizabeth Pennisi, Science 323(5910):27 (2 January 2009).
A large-scale study in Australia's Great Barrier Reef, reported on page 116 (Declining Coral Calcification on the Great Barrier Reef, Glenn De'ath, Janice M. Lough, and Katharina E. Fabricius, Science 323(5910):116) of this week's issue of Science, has revealed that the rate at which corals absorb calcium from seawater to calcify their hard skeletons has declined precipitously in the past 20 years, slowing coral growth.

Coastal eutrophication: Whether N and/or P should be abated depends on the dynamic mass balance, Andreas C. Bryhn1 and Lars Håkanson, PNAS 106(1):E3 (January 6, 2009).
Whether nitrogen (N) and/or phosphorus (P) should be abated to counteract coastal eutrophication remains controversial. System-wide lake experiments presented in PNAS have shown that P control was essential for dampening algal blooms whereas N control only strengthened the competitive advantage of cyanobacteria and increased fixation of dissolved N2 from the atmosphere.

Reply to Bryhn and Håkanson: Models for the Baltic agree with our experiments and observations in lakes, D. W. Schindlera,1 and R. E. Heckyb, PNAS 106(1):E4 (January 6, 2009).
As Bryhn and Håkanson state (1), their mass-balance modeling yields results that agree with our observations (2) based on a long-term lake experiment and a recovery in part of the Baltic resulting from phosphorus control (3). Other recent papers (4) also support our conclusion that phosphorus control deserves a second look in coastal systems, at least those containing brackish water. As the authors (1) point out, control of nitrogen in runoff could be costly enough to cripple agriculture in some areas. We agree with them that until ecosystem-scale evidence is obtained, "N abatement is a very expensive shot in the dark that may favor cyanobacteria instead of the water quality."

Increasing Crop Productivity to Meet Global Needs for Feed, Food, and Fuel, Michael D. Edgerton, Plant Physiol. 149:7-13 (2009).

Translational Biology: From Arabidopsis Flowers to Grass Inflorescence Architecture, Beth E. Thompson and Sarah Hake, Plant Physiol. 149:38-45 (2009).

Hormonal Regulation of Branching in Grasses, Paula McSteen, Plant Physiol. 149:46-55 (2009).

Mechanisms of Floral Induction in Grasses: Something Borrowed, Something New, Joseph Colasanti and Viktoriya Coneva, Plant Physiol. 149:56-62 (2009).

Poaceae Genomes: Going from Unattainable to Becoming a Model Clade for Comparative Plant Genomics, C. Robin Buell, Plant Physiol. 149:111-116 (2009).

Synergy of Two Reference Genomes for the Grass Family, Joachim Messing, Plant Physiol. 149:117-124 (2009).

Comparative Genomics of Grasses Promises a Bountiful Harvest, Andrew H. Paterson, John E. Bowers, Frank A. Feltus, Haibao Tang, Lifeng Lin, and Xiyin Wang, Plant Physiol. 149:125-131 (2009).

Genomic and Genetic Database Resources for the Grasses, Kevin L. Childs, Plant Physiol. 149:132-136 (2009).

Foxtail Millet: A Sequence-Driven Grass Model System, Andrew N. Doust, Elizabeth A. Kellogg, Katrien M. Devos, and Jeffrey L. Bennetzen, Plant Physiol. 149:137-141 (2009).

Cereal Germplasm Resources, Martin M. Sachs, Plant Physiol. 149:148-151 (2009).

Resources for Virus-Induced Gene Silencing in the Grasses, Steven R. Scofield and Richard S. Nelson, Plant Physiol. 149:152-157 (2009).

GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses, Alper Yilmaz, Milton Y. Nishiyama, Jr., Bernardo Garcia Fuentes, Glaucia Mendes Souza, Daniel Janies, John Gray, and Erich Grotewold, Plant Physiol. 149:171-180 (2009).

Genome-Wide Analysis of MIKCC-Type MADS Box Genes in Grapevine, Jose Diaz-Riquelme, Diego Lijavetzky, Jose M. Martinez-Zapater, and Maria Jose Carmona, Plant Physiol. 149:354-369 (2009).