Late March 2009 papers

Some interest papers.

Plant cell biology: When autumn falls, Simon Bishop, Nature Reviews Molecular Cell Biology 10:238-239.

Trifurcate feed-forward regulation of age-dependent cell death involving miR164 in Arabidopsis, Jin Hee Kim, Hye Ryun Woo, Jeongsik Kim, Pyung Ok Lim, In Chul Lee, Seung Hee Choi, Daehee Hwang, Hong Gil Nam, Science 323:1053–1057 (2009).

Aquaculture: Future fish, Daniel Cressey, Nature 458(7237):398-400 (26 March 2009).
The only way to meet the increasing demand for fish is through aquaculture. Daniel Cressey explores the challenges for fish farmers and what it means for dinner plates in 2030.

Structural biology: Spliceosome subunit revealed, Charles C. Query, Nature 458(7237):418-419 (26 March 2009).
The spliceosome enzyme binds to RNA transcripts at splice sites and removes intron sequences. The crystal structure of a spliceosome subunit shows how the enzyme recognizes one end of the intron.

The ubiquitin system, Nature 458(7237):421–467 (26 March 2009).
The central role of ubiquitin in cell-cycle regulation, DNA repair, cell growth, signalling and immune function is starting to become clear right down to the molecular level. Identifying irregularities in the system has opened up opportunities in drug discovery, and in diagnostics and treatment for a range of disorders, from cancer to neurodegeneration.

Crystal structure of human spliceosomal U1 snRNP at 5.5 Å resolution, Daniel A. Pomeranz Krummel et al., Nature 458(7237):475-480 (26 March 2009).
In eukaryotes, many genes contain one or more introns — sequences that are transcribed into mRNA, but which are then excised before the mRNA is translated into protein. Multiprotein–RNA complexes called snRNPs are the machinery that clips these introns out. This study presents the structure of the U1 snRNP, which assembles at the 5′ end of the intron; the subunit interactions suggest a model by which the snRNP is assembled and the 5′ splice site is recognized.

PROFILE: JORGE CHAM: Piled Higher and Deeper: The Everyday Life of a Grad Student, Science 323(5922):1668 - 1669 (27 March 2009).
Jorge Cham's comic strip, capturing the trials and tribulations of grad school, became so popular that he left the lab for a career as a cartoonist and lecturer.

CHEMISTRY: Producing Transportation Fuels with Less Work, D. Hildebrandt et al., Science 323(5922):1680 - 1681 (27 March 2009).
New reaction chemistry may reduce the energy input and carbon dioxide emissions from processes that convert coal into liquid fuels.

Conserved intragenic elements were critical for the evolution of the floral C-function, Barry Causier, Desmond Bradley, Holly Cook and Brendan Davies, The Plant Journal 58(1):41 - 52.

Glutaredoxin Functions in Floral Development, Nancy R. Hofmann, Plant Cell 21:363 (2009).

The Future of Science: Food and Water for Life, Nancy A. Eckardt, Eleonora Cominelli, Massimo Galbiati, and Chiara Tonelli, Plant Cell 21:368-372 (2009).

Nuclear Activity of ROXY1, a Glutaredoxin Interacting with TGA Factors, Is Required for Petal Development in Arabidopsis thaliana, Shutian Li, Andrea Lauri, Mark Ziemann, Andrea Busch, Mrinal Bhave, and Sabine Zachgo, Plant Cell 21:429-441 (2009).

A Bacterial-Type ABC Transporter Is Involved in Aluminum Tolerance in Rice, Chao Feng Huang, Naoki Yamaji, Namiki Mitani, Masahiro Yano, Yoshiaki Nagamura, and Jian Feng Ma,
Plant Cell 21:655-667 (2009).

A Novel Plant Leucine-Rich Repeat Receptor Kinase Regulates the Response of Medicago truncatula Roots to Salt Stress, Laura de Lorenzo, Francisco Merchan, Philippe Laporte, Richard Thompson, Jonathan Clarke, Carolina Sousa, and Martin Crespi, Plant Cell 21:668-680 (2009).

Cheap third-generation sequencing, Nicole Rusk, Nature Methods 6(4):244.
By covalently attaching cyclodextrin to a hemolysin nanopore, researchers show single-molecule, label-free sequencing at very high accuracy.

Snapshots of proteins at work, Allison Doerr, Nature Methods 6(4):246.
Two groups extend the boundaries of in-cell nuclear magnetic resonance spectroscopy.

QPCR without the 'P', Irene Kaganman, Nature Methods 6(4):250.
With the addition of a ligand-sensing aptamer sequence, a self-replicating RNA enzyme system enables general molecular detection, analogous to that of quantitative PCR.

Journeys across the membrane, Nathan Blow, Nature Methods 6(4):305-309.
From high-throughput electroporation platforms capable of transfecting thousands of different cells in a day, to nanowires that puncture and deliver DNA to just a single cell, new technology is emerging to help researchers with their changing gene delivery needs.

Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD™ system, Anjali Shah, Nature Methods 6(4).
Chromatin immunoprecipitation (ChIP) is a technique for identifying and characterizing elements in protein-DNA interactions involved in gene regulation or chromatin organization. Microarray platforms provide a method for 'global' ChIP analysis, but direct sequencing of enriched fragments has proven a more effective means for determining locations of DNA-binding proteins along the genome in an unbiased manner. The massively parallel sequencing capacity, high accuracy and flexibility of the SOLiD™ system make it well suited for ChIP-sequencing (ChIP-Seq) applications.