Feb 2009 papers

Here are some interest papers.

Synthetic biology: The yin and yang of nature, Jeff Gore & Alexander van Oudenaarden, Nature 457:271-272 (15 January 2009).
Oscillations in gene expression regulate various cellular processes and so must be robust and tunable. Interactions between both negative and positive feedback loops seem to ensure these features.

Plant development: Genes turn on for a new leaf, Mary Muers, Nature Reviews Genetics 10, 74-75 (February 2009). A Research Highlights for following paper:
A Conserved Molecular Framework for Compound Leaf Development, Thomas Blein, Amada Pulido, Aurélie Vialette-Guiraud, Krisztina Nikovics, Halima Morin, Angela Hay, Ida Elisabeth Johansen, Miltos Tsiantis, Patrick Laufs, Science 322(5909):1835 - 1839 (19 December 2008).

Small silencing RNAs: an expanding universe, Megha Ghildiyal & Phillip D. Zamore, Nature Reviews Genetics 10:94-108 (February 2009).

The NAC-domain transcription factor GOBLET specifies leaflet boundaries in compound tomato leaves, Yael Berger, Smadar Harpaz-Saad, Arnon Brand, Hadas Melnik, Neti Sirding, John Paul Alvarez, Michael Zinder, Alon Samach, Yuval Eshed, and Naomi Ori, Development 136:823-832.

Alterations in the Endogenous Ascorbic Acid Content Affect Flowering Time in Arabidopsis
Simeon O. Kotchoni, Katherine E. Larrimore, Madhumati Mukherjee, Chase F. Kempinski, and Carina Barth, Plant Physiol. 149:803-815.

The Arabidopsis Abscisic Acid Catabolic Gene CYP707A2 Plays a Key Role in Nitrate Control of Seed Dormancy, Theodoros Matakiadis, Alessandro Alboresi, Yusuke Jikumaru, Kiyoshi Tatematsu, Olivier Pichon, Jean-Pierre Renou, Yuji Kamiya, Eiji Nambara,
and Hoai-Nam Truong, Plant Physiol. 149:949-960.

Histone H2B Deubiquitination Is Required for Transcriptional Activation of FLOWERING LOCUS C and for Proper Control of Flowering in Arabidopsis, Robert Jeffrey Schmitz, Yosuke Tamada, Mark Robert Doyle, Xiaoyu Zhang, and Richard Mark Amasino, Plant Physiol. 149:1196-1204.

Merck joins the biotech game, Victor Bethencourt, Nature Biotechnology 27:104.

GM poplars to grow next door, Hayley Birch, Nature Biotechnology 27:107.

Land use stirs biofuels ruckus, Susan Kim, Nature Biotechnology 27:109.

Proprietary science, open science and the role of patent disclosure: the case of zinc-finger proteins, Subhashini Chandrasekharan, Sapna Kumar, Cory M Valley & Arti Rai, Nature Biotechnology 27:140 - 144.
A closer look at the large patent estate now covering both the engineering and use of zinc-finger proteins.

Prediction of high-responding peptides for targeted protein assays by mass spectrometry, Vincent A Fusaro, D R Mani, Jill P Mesirov & Steven A Carr, Nature Biotechnology 27:190 - 198.
Development of sensitive mass spectrometry–based assays for complex biofluids depends on the ability to identify signature peptides that produce the strongest signals. Fusaro et al. use protein physicochemical properties to predict high-responding peptides in data obtained from complex samples such as plasma.

Splice-site pairing is an intrinsically high fidelity process, Kristi L. Fox-Walsh and Klemens J. Hertel, PNAS 2009 106:1766-1771.




RICHARD RICHARDS PROFILE: Making Every Drop Count in the Buildup to a Blue Revolution, Science 323(5917):1004 - 1005 (20 February 2009).
Richard Richards, a geneticist at CSIRO Plant Industry, is breeding wheat varieties that can tough out prolonged droughts--and keep people fed.

ATMOSPHERIC SCIENCE: A Matter of Humidity, A. E. Dessler and S. C. Sherwood, Science 323(5917):1020 (20 February 2009).
How strong a part does water vapor play in global warming?

CELL BIOLOGY: Stress Response and Aging, L. R. Saunders and E. Verdin, Science 323(5917):1021 (20 February 2009).
Transcriptional regulators that respond to stress also influence life span.

A Genetic Defect Caused by a Triplet Repeat Expansion in Arabidopsis thaliana, Sridevi Sureshkumar, Marco Todesco, Korbinian Schneeberger, Ramya Harilal, Sureshkumar Balasubramanian, Detlef Weigel, Science 323(5917):1060-1063 (20 February 2009).
A strain of Arabidopsis provides a plant model for the harmful effects of repeat nucleotide expansions in populations.

Molecular processes underlying the floral transition in the soybean shoot apical meristem, Chui E. Wong, Mohan B. Singh, Prem L. Bhalla, The Plant Journal 57(5):832 - 845.

MERISTEM-DEFECTIVE, an RS domain protein, is required for the correct meristem patterning and function in Arabidopsis, Stuart A. Casson, Jennifer F. Topping, Keith Lindsey, The Plant Journal 57(5):857-869.

Resetting and regulation of FLOWERING LOCUS C expression during Arabidopsis reproductive development, Jean Choi, Youbong Hyun, Min-Jeong Kang, Hye In Yun, Jae-Young Yun, Clare Lister, Caroline Dean, Richard M. Amasino, Bosl Noh, Yoo-Sun Noh, Yeonhee Choi, The Plant Journal 57(5):918 - 931.

How plant defence gets hairy, Development 136:e606.

Jasmonic acid control of GLABRA3 links inducible defense and trichome patterning in Arabidopsis, Yuki Yoshida, Ryosuke Sano, Takuji Wada, Junji Takabayashi, and Kiyotaka Okada, Development 136:1039-1048.

Epigenetic inheritance during the cell cycle, Aline V. Probst, Elaine Dunleavy & Geneviéve Almouzni, Nature Reviews Molecular Cell Biology 10(3):192.
Epigenetic inheritance concerns the mechanisms that ensure the transmission of epigenetic marks from mother to daughter cell. Chromatin modifications and nuclear organization are candidate epigenetic marks — whether they fulfil the criterion of heritability and what mechanisms ensure their propagation is an area of intensive research.

Single proteins might have dual but related functions in intracellular and extracellular microenvironments, Derek C. Radisky, Melody Stallings-Mann, Yohei Hirai & Mina J. Bissell, Nature Reviews Molecular Cell Biology 10(3):228.
Maintenance of organ homeostasis and control of appropriate responses to environmental alterations requires the coordination of cellular functions and tissue organization. This coordination could be achieved by proteins that can have distinct but linked functions on both sides of the plasma membrane.

Differential chromatin marking of introns and expressed exons by H3K36me3, Paulina Kolasinska-Zwierz, Thomas Down, Isabel Latorre, Tao Liu, X Shirley Liu and Julie Ahringer, Nature Genetics 41(3):376 - 381.
Julie Ahringer and colleagues show that, in C. elegans, exons are preferentially marked with H3K36me3 relative to introns, and that the difference in H3K36me3 marking between exons and introns is evolutionarily conserved in human and mouse.

Reverse ChIP, Nicole Rusk, Nature Methods 6(3):187.
The combination of a DNA probe and mass spectrometric analysis allows the unbiased identification of chromatin-associated proteins.

Mimicking a pore, Amy Donner, Nature Methods 6(3):188 - 189.
A functionalized polycarbonate nanosorter mimics fundamental properties of the nuclear pore complex.

Quantitative interaction proteomics using mass spectrometry, Alexander Wepf, Timo Glatter, Alexander Schmidt, Ruedi Aebersold & Matthias Gstaiger, Nature Methods 6(3):203 - 205.
Absolute quantitative information about the stoichiometry of protein complex components can be obtained with a modified affinity purification–mass spectrometry method, as demonstrated for the human protein phosphatase 2A network.

Small RNAs: biology's brave new world, Nathan Blow, Nature Methods 6(3):231 - 235.
Small RNA discovery and profiling efforts are dramatically reshaping fundamental concepts of how genes are regulated and are leading to new tools for studying gene function.