Mid-Dec 2008 papers

Here are some interested papers in mid-Dec., 2008.

Europe lags, US leads 2nd-generation biofuels, Cormac Sheridan, Nature Biotech 26(12):1319 - 1321 (December 2008).

Biomarkers' double edge, Jeffrey L Fox, Nature Biotech 26(12):1322 (December 2008).

Automated de novo protein sequencing of monoclonal antibodies, Nuno Bandeira, Victoria Pham, Pavel Pevzner, David Arnott and Jennie R Lill, Nature Biotech 26(12):1336 - 1338 (December 2008).

Antibody patenting without antibodies: a global trend, Kazunori Hashimoto & Tomomi Aida, Nature Biotech 26(12):1341 - 1343 (December 2008).
Granting human gene patents that include broad antibody claims without any experimental antibody production makes the gene patent issue more complex.

Design and analysis of ChIP-seq experiments for DNA-binding proteins, Peter V Kharchenko, Michael Y Tolstorukov & Peter J Park, Nature Biotech 26(12):1351 - 1359 (December 2008).
Critical considerations in the design and analysis of ChIP-seq experiments include how to align sequenced tags to the genome, how to detect binding sites and how to estimate the number of tags needed to confidently determine where a protein binds DNA. ....

TRANSCRIPTION: Gene Expression--Where to Start? , Stephen Buratowski, , Science 322(5909):1804 (19 December 2008).
Transcription just got noisier with the discovery of short RNAs that are synthesized at or near DNA regions that also initiate full-length RNAs.

The Circadian Clock in Arabidopsis Roots Is a Simplified Slave Version of the Clock in Shoots, A. B. James et al., Science 322(5909):1832 - 1835 (19 December 2008).
A simpler plant circadian clock, which normally has three interlocking feedback loops, is used in the roots, with one feedback loop regulating only a few genes.

A Conserved Molecular Framework for Compound Leaf Development, T. Blein et al., Science 322(5909):1835 - 1839 (19 December 2008).
A family of transcription factors controls the formation of leaflets and lobes in complex leaves in distantly related plants by controlling outgrowth from leaf margins.

Increasing corn for biofuel production reduces biocontrol services in agricultural landscapes, Douglas A. Landis, Mary M. Gardiner, Wopke van der Werf, and Scott M. Swinton, PNAS 105(51):20552-20557 (December 23, 2008).

Quantitative genetics, Nature Insight 456(7223):719–744 (December 2008).
Recent revolutions in genomic technologies have led to a renewed interest in quantitative genetics.

Next-generation genetics in plants, Magnus Nordborg & Detlef Weigel, Nature Insight 456(7223):720 - 723 (December 2008).

Reverse engineering the genotype–phenotype map with natural genetic variation, Matthew V. Rockman, Nature Insight 456(7223):738 (December 2008).

Plant hormone study pulled: Canadian lab retracts work on abscisic acid, Emma Marris, Nature 456(7223):683 (10 December 2008).
Two years ago, three papers made a splash in the plant biology world by identifying protein receptors for abscisic acid (ABA), a key hormone in plant physiology. This week, Nature is retracting one of those papers1 after reports that the work could not be replicated.

FCA does not bind abscisic acid, Joanna M. Risk, Richard C. Macknight and Catherine L. Day, Nature 456(7223):E5-E6 (11 December 2008).