July 2009 papers

Gee! It is almost end of July and I did not even put anything in yet. I am so tired this month. Anyway I will start to put some interest papers in.

Lack of direct evidence for the carbon-starvation hypothesis to explain drought-induced mortality in trees, Anna Sala, PNAS 106(26):E68.

Reply to Sala: Temperature sensitivity in drought-induced tree mortality hastens the need to further resolve a physiological model of death, Henry D. Adams, Maite Guardiola-Claramonte, Greg A. Barron-Gafford, Juan Camilo Villegas, David D. Breshears, Chris B. Zou, Peter A. Troch, and Travis E. Huxman, PNAS 106(26):E69.

Biogeochemistry: Climatic plant power, Yves Goddéris and Yannick Donnadieu, Nature 460:40-41.
Levels of atmospheric carbon dioxide constrain vegetation types and thus also non-biological uptake during rock weathering. That's the reasoning used to explain why CO2 levels did not fall below a certain point in the Miocene.

How Sweet It Is: Identification of Vacuolar Sucrose Transporters, Aleel K. Grennan and Jeremy Gragg, Plant Physiol. 2009;150 1109-1110.

A Versatile Zero Background T-Vector System for Gene Cloning and Functional
Genomics, Songbiao Chen, Pattavipha Songkumarn, Jianli Liu, and Guo-Liang Wang
Plant Physiol. 2009;150 1111-1121.

A Visual Reporter System for Virus-Induced Gene Silencing in Tomato Fruit Based on Anthocyanin Accumulation, Diego Orzaez, Aurora Medina, Sara Torre, Josefina Patricia, Fernandez-Moreno, Jose Luis Rambla, Asun Fernandez-del-Carmen, Eugenio Butelli, Cathie Martin, and Antonio Granell, Plant Physiol. 2009;150 1122-1134.

The Role of Annexin 1 in Drought Stress in Arabidopsis, Dorota Konopka-Postupolska, Greg Clark, Grazyna Goch, Janusz Debski, Krzysztof Floras, Araceli Cantero, Bartlomiej Fijolek, Stanley Roux, and Jacek Hennig, Plant Physiol. 2009;150 1394-1410.

Two Alternatively Spliced Isoforms of the Arabidopsis SR45 Protein Have Distinct Roles during Normal Plant Development, Xiao-Ning Zhang and Stephen M. Mount
Plant Physiol. 2009;150 1450-1458.

FRIGIDA Delays Flowering in Arabidopsis via a Cotranscriptional Mechanism Involving Direct Interaction with the Nuclear Cap-Binding Complex, Nuno Geraldo, Isabel Baurle, Shin-ichiro Kidou, Xiangyang Hu, and Caroline Dean, Plant Physiol. 2009;150 1611-1618.

Green Life Through Time, Jonathan P. Wilson, Science 325(5936):36 - 37.
An expansion and update of Taylor and Taylor's classic 1993 book, this lavishly illustrated volume offers a comprehensive survey of fossil plants and fungi.

Sweet Silencing, Jeffrey A. Simon, Science 325(5936):45 - 46.
A sugar molecule plays an unexpected role in controlling gene silencing by modifying repressor proteins.

When Earth greened over, Eric Hand, Nature 460:161.
Explosion of animal life could have been triggered by blanket of vegetation.

Adaptive prediction of environmental changes by microorganisms, Amir Mitchell et al., Nature 460:220-224.
Habitats where environmental change occurs in a reliable order offer microorganisms the opportunity to prepare in advance. Here, in both the bacterium Escherichia coli and the yeast Saccharomyces cerevisiae, stimuli that typically appear early in the ecology of the organism are shown to induce genes that are useful for coping with conditions that normally occur later, a process that is also shown to improve fitness.

Plain English: Free service helps scientists get published, Nature 460:295.
Two young researchers have launched a free manuscript-editing service to help scientists from developing countries get papers published in English-language journals. Justin Chakma, a research analyst at the McLaughlin-Rotman Centre for Global Health in Toronto, Canada, and Alexander Patananan, a biochemistry doctoral student at the University of California, Los Angeles, set up SciEdit earlier this year as a spin-off of the Journal of Young Investigators, an international student-run, peer-reviewed journal. In choosing which papers to improve, it assesses the merit of the science, not just the use of English. To date, SciEdit has accepted 10 manuscripts from India, South Africa, Pakistan, China and Nepal.

Glycinebetaine-induced water-stress tolerance in codA-expressing transgenic indica rice is associated with up-regulation of several stress responsive genes, Hitesh Kathuria, Jitender Giri, Karaba N. Nataraja, Norio Murata, Makarla Udayakumar, Akhilesh K. Tyagi, Plant Biotechnology 7(6):512 - 526.

The fungal RNA-binding protein Rrm4 mediates long-distance transport of ubi1 and rho3 mRNAs, Julian König, Sebastian Baumann, Janine Koepke, Thomas Pohlmann, Kathi Zarnack and Michael Feldbrügge, EMBO 28:1855 - 1866.

DOE's Push to Train a New Generation Falters in House, Science 325(5937):130 - 131.
Secretary of Energy Steven Chu has proposed a 10-year, $1.7 billion education program called RE-ENERGYSE to help the United States find the talent to fuel its clean-energy economy. But Congress may prefer to wait until next year.

Tofu Was Just a Start, Michael A. Grusak, Science 325(5937):150.
The contributors explore the range of foods made from soybean and the other ways soy products enter our meals, highlighting how important these foods are and how important they may become.

Drug Discovery and Natural Products: End of an Era or an Endless Frontier?, J. W.-H. Li and J. C. Vederas, Science 325(5937):161 - 165.

Ozone suppresses soil drying- and abscisic acid (ABA)-induced stomatal closure via an ethylene-dependent mechanism, SALLY WILKINSON, WILLIAM J. DAVIES, Plant, Cell & Environment 32(8):949 - 959.

Report claims no yield advantage for Bt crops, Cormac Sheridan, Nature Biotechnology 27:588 - 589 (2009).
A controversial report claims that traits introduced to food crops by genetic engineering (GE) have had, at best, a minor impact on yield.

NCBI Peptidome: a new public repository for mass spectrometry peptide identifications, Douglas J Slotta, Tanya Barrett and Ron Edgar, Nature Biotechnology 27:600 - 601.

Biomarker validation by targeted mass spectrometry, Martin McIntosh and Matthew Fitzgibbon, Nature Biotechnology 27:622 - 623.
A multilaboratory study demonstrates the potential for establishing quantitative targeted proteomic assays for moderately to highly abundant plasma proteins.

Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream, Nikos C Kyrpides, Nature Biotechnology 27:627 - 632.
Now that ~1,000 microbial genomes have been sequenced, Nikos Kyrpides reflects on the past decade of microbial genomics and extrapolates forward to propose solutions to meeting challenges in the field.

Climate change: Beyond the CO2 connection, Rainer Zahn, Nature 460:335-336 (16 July 2009).
At times in the past, mobile ocean fronts in the subtropics have exercised an influence on the magnitude of climate change by decoupling temperature from levels of carbon dioxide in the atmosphere.

Global patterns of speciation and diversity, M. A. M. de Aguiar et al., Nature 460, 384-387 (16 July 2009).
The question of why biological diversity is spread in characteristic patterns is perhaps the biggest problem in ecology. In recent years, the 'neutral theory' of biodiversity has modelled the distribution of species in a very simple way, without reference to species interactions or history. Sexual reproduction, mutation and dispersal are now introduced to the simulation of populations; the resulting predictions correlate well with real data sets.

Beyond the Type Genome: Discovery of Novel Avirulence Genes in the Rice: Blast Fungus by Genomic Resequencing and Genetic Association Studies, Jennifer Mach, Plant Cell 21:1325.

Membrane Rafts and Virus Movement in Plant Cells, Nancy A. Eckardt, Plant Cell 21:1326.

PUCHI and Floral Meristem Identity, Gregory Bertoni, Plant Cell 21:1327.

A Role for Arabidopsis PUCHI in Floral Meristem Identity and Bract Suppression, Md. Rezaul Karim, Atsuko Hirota, Dorota Kwiatkowska, Masao Tasaka, and Mitsuhiro Aida, Plant Cell 21:1360-1372.
Acquisition of flower identity in Arabidopsis is associated with the
switch from an indeterminate to a determinate growth pattern and
suppression of a subtending leaf called a bract. It is shown that the
AP2/EREBP gene PUCHI, together with the NPR1-like signaling genes
BOP1 and BOP2, are required for these processes, possibly
through position-specific activation of the floral regulators LFY
and AP1.

Association Genetics Reveals Three Novel Avirulence Genes from the Rice Blast Fungal Pathogen Magnaporthe oryzae, Kentaro Yoshida, Hiromasa Saitoh, et al., Plant Cell 21:1573-1591.
This work uses genome resequencing, large-scale association genetics, and
in vivo functional complementation to identify avirulence proteins
AVR-Pia, AVR-Pii, and AVR-Pik/km/kp from among a large
set of candidate secreted proteins from the major rice pathogen
Magnaporthe oryzae.

Beneficial Biofuels—The Food, Energy, and Environment Trilemma, D. Tilman et al., Science 325(5938):270 - 271.
Exploiting multiple feedstocks, under new policies and accounting rules, to balance biofuel production, food security, and greenhouse-gas reduction.

Neutralizing Toxic RNA, Thomas A. Cooper, Science 325(5938):272.
Oligonucleotides that target aggregates of RNA and protein show potential for treating myotonic dystrophy.

What Drives Climate Flip-Flops? A. Timmermann and L. Menviel, Science 325(5938):273.
A numerical modeling study questions the validity of a key paradigm in rapid climate change studies.

The carbon count, Nature 460:436 (23 July 2009).
Scientists need better Earth-monitoring tools to see whether climate policies are working.

ExxonMobil invests in algae for biofuel, Nature 460:449 (2009).
Oil and gas company ExxonMobil, whose chief executive Rex Tillerson called the idea of ethanol as a biofuel "moonshine" in 2007, last week announced a US$600-million research alliance to develop biofuels from photosynthetic algae.