Targeted Mutagenesis of the Multicopy Gene Family in Allotetraploid Reduces Pungency in Fresh Leaves across Environments.

Recent breeding efforts in have focused on the development of new oilseed feedstock crop for biofuels (e.g., ethanol, biodiesel, bio-jet fuel), bio-industrial uses (e.

SHAPE-directed discovery of potent shRNA inhibitors of HIV-1.

The RNA interference (RNAi) pathway can be exploited using short hairpin RNAs (shRNAs) to durably inactivate pathogenic genes. Prediction of optimal target sites is notoriously inaccurate and current approaches applied to HIV-1 show weak correlations with virus inhibition. In contrast, using a high-content model for disrupting pre-existing intramolecular structure in the HIV-1 RNA, as achievable using high-resolution SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) chemical probing information, we discovered strong correlations between inhibition of HIV-1 production in a quantitative cell-based assay and very simple thermodynamic features in the target RNA.

Architecture and secondary structure of an entire HIV-1 RNA genome.

Single-stranded RNA viruses encompass broad classes of infectious agents and cause the common cold, cancer, AIDS and other serious health threats. Viral replication is regulated at many levels, including the use of conserved genomic RNA structures. Most potential regulatory elements in viral RNA genomes are uncharacterized.

Status of the Riparian ecosystem in the upper San Pedro River, Arizona: application of an assessment model.

A portion of Arizona's San Pedro River is managed as a National Riparian Conservation Area but is potentially affected by ground-water withdrawals beyond the conservation area borders. We applied an assessment model to the Conservation Area as a basis for monitoring long-term changes in riparian ecosystem condition resulting from changes in river water availability, and collected multi-year data on a subset of the most sensitive bioindicators. The assessment model is based on nine vegetation bioindicators that are sensitive to changes in surface water or ground water.

Ligand-mediated anticodon conformational changes occur during tRNA methylation by a TrmD methyltransferase.

Orthologs of TrmD, G37 tRNA methyltransferases, have been analyzed with regard to post-tRNA binding events required to move the residue G37 in proximity to bound AdoMet for catalysis. This was approached initially by probing tRNA with T2 nuclease or Pb acetate in the presence, then absence, of Escherichia coli TrmD protein. Cleavage patterns clearly show that portions of the anticodon loop phosphodiester backbone are protected from cleavage only in the presence of sinefungin, a potent AdoMet analogue.

Characterization of Streptococcus pneumoniae TrmD, a tRNA methyltransferase essential for growth.

Down-regulation of expression of trmD, encoding the enzyme tRNA (guanosine-1)-methyltransferase, has shown that this gene is essential for growth of Streptococcus pneumoniae. The S. pneumoniae trmD gene has been isolated and expressed in Escherichia coli by using a His-tagged T7 expression vector.

Insights into catalysis by a knotted TrmD tRNA methyltransferase.

The crystal structure of Escherichia coli tRNA (guanosine-1) methyltransferase (TrmD) complexed with S-adenosyl homocysteine (AdoHcy) has been determined at 2.5A resolution. TrmD, which methylates G37 of tRNAs containing the sequence G36pG37, is a homo-dimer.

Cluster analysis of structural stage classes to map wildland fuels in a Madrean ecosystem.

Geospatial information technology is changing the nature of fire mapping science and management. Geographic information systems (GIS) and global positioning system technology coupled with remotely sensed data provide powerful tools for mapping, assessing, and understanding the complex spatial phenomena of wildland fuels and fire hazard. The effectiveness of these technologies for fire management still depends on good baseline fuels data since techniques have yet to be developed to directly interrogate understory fuels with remotely sensed data.