Ealy May 2009 papers

Some interest papers.

Sequence is not everything, Natalie de Souza, Nature Methods 6:320 - 321.
A new algorithm for identifying evolutionary constraint incorporates information on local DNA topology, and leads to the finding that this topology is conserved across species.

A Mycorrhizal-Specific Ammonium Transporter from Lotus japonicus Acquires Nitrogen Released by Arbuscular Mycorrhizal Fungi, Mike Guether, Benjamin Neuhauser, Raffaella Balestrini, Marek Dynowski, Uwe Ludewig, and Paola Bonfante, Plant Physiol. 150:73-83

Strigolactone Acts Downstream of Auxin to Regulate Bud Outgrowth in Pea and
Arabidopsis, Philip B. Brewer, Elizabeth A. Dun, Brett J. Ferguson, Catherine Rameau, and Christine A. Beveridge, Plant Physiol. 150:482-493.

Regulation and function of root exudates, DAYAKAR V. BADRI, JORGE M. VIVANCO, Plant, Cell & Environment 32(6):666-681.

Nitrate and glutamate as environmental cues for behavioural responses in plant roots, BRIAN G. FORDE, PIA WALCH-LIU, Plant, Cell & Environment 32(6):682-693.

The control of shoot branching: an example of plant information processing, OTTOLINE LEYSER, Plant, Cell & Environment 32(6):694-703.

What's Bugging Plants?, P. J. Hines and L. M. Zahn, Science 324(5928):741.

Innate Immunity in Plants: An Arms Race Between Pattern Recognition Receptors in Plants and Effectors in Microbial Pathogens, T. Boller and S. Y. He, Science 324(5928):742.

To Nibble at Plant Resistance Proteins, F. L. W. Takken and W. I. L. Tameling, Science 324(5928):744.

Plant-Microbe Interactions: Chemical Diversity in Plant Defense, P. Bednarek and A. Osbourn, Science 324(5928):746.

Terrific Protein Traffic: The Mystery of Effector Protein Delivery by Filamentous Plant Pathogens, R. Panstruga and P. N. Dodds, Science 324(5928):748.

Hormone (Dis)harmony Moulds Plant Health and Disease, M. R. Grant and J. D. G. Jones, Science 324(5928):750.

Reprogramming Plant Cells for Endosymbiosis, G. E. D. Oldroyd et al., Science 324(5928):753.

Coevolution of Plants and Their Pathogens in Natural Habitats, J. J. Burdon and P. H. Thrall, Science 324(5928):755.

An Invasive Plant Paradox, M. E. Rout and R. M. Callaway, Science 324(5928):734 - 735.
One reason that invasive plants may thrive in new environments is their interactions with soil microbes that increase nitrogen cycling.

The function of non-coding RNAs in genomic imprinting, Martha V. Koerner, Florian M. Pauler, Ru Huang, and Denise P. Barlow, Development 2009;136 1771-1783.

How to map billions of short reads onto genomes, Cole Trapnell and Steven L Salzberg, Nature Biotechnology 27(5):455 - 457.
Mapping the vast quantities of short sequence fragments produced by next-generation sequencing platforms is a challenge. What programs are available and how do they work?

Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression, Jinkuk Kim and David P Bartel, Nature Biotechnology 27(5):472 - 477.
Single-nucleotide polymorphisms in microRNA target sites can disrupt the effects of the microRNA. Kim and Bartel use sequencing to investigate this phenomenon on a large scale and find that such polymorphisms generate gene-regulatory diversity in mice.

Transgenic barley (Hordeum vulgare L.) expressing the wheat aluminium resistance gene (TaALMT1) shows enhanced phosphorus nutrition and grain production when grown on an acid soil, Emmanuel Delhaize, Phillip Taylor, Peter J. Hocking, Richard J. Simpson, Peter R. Ryan, Alan E. Richardson, Plant Biotechnology Journal 7(5):391 - 400.

The future of the human SNP identification: Which individuals to sequence? Juergen K. V. Reichardt and Ruty Mehrian-Shai