Hot off the presses! May 01 Trends Pl Sci

The May 01 issue of the Trends Pl Sci is now up on Pubget (About Trends Pl Sci): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends Pl Sci 16(5):i (2011)
  
• Combining phenotypic data from ordinal rating scales in multiple plant experiments
  - Trends Pl Sci 16(5):235-237 (2011)
  
• Self-incompatibility: Smi silences through a novel sRNA pathway
  - Trends Pl Sci 16(5):238-241 (2011)
  Self-incompatibility in Brassicaceae is determined by the interaction between S-Locus Protein 11 (SP11) on the pollen and S-receptor kinase (SRK) in the stigma. Pollen from heterozygotes generally displays products of both SP11 alleles, but in some heterozygotes SP11 expression is monoallelic, with one allele (SP11R) being silenced by promoter methylation. An exciting development in understanding the mechanism behind monoallelic silencing came recently when Y. Tarutani et al. [Nature 2010;466:983–986] identified a 24-nucleotide sRNA (termed Smi) derived from a non-coding gene within the dominant S-haplotype, and suggested that Smi directs promoter methylation. We propose that rather than having a direct effect on DNA methylation, Smi is the first step in a novel cis-acting siRNA pathway that directs widespread monoallelic SP11R promoter methylation.
• MicroRNA misregulation: an overlooked factor generating somaclonal variation?
  - Trends Pl Sci 16(5):242-248 (2011)
  Somaclonal variation is an important phenomenon that can be observed at high levels in plant tissue culture. Although known to science since plant cell culture techniques were first developed, its origins remain mysterious. Here, we propose that misregulation of microRNAs and small RNA pathways can make a significant contribution to the phenomenon. For many reasons, microRNAs and related small RNAs appear ideal candidates. Their mode of action gives them disproportionate influence over the transcriptome, proteome and epigenome. They regulate important developmental and physiological events such as meristem formation, phase changes and hormone responses. However, the genomic locations of microRNA genes and their unique biogenesis might make them unusually susceptible to aberrant regulation in vitro.
• Jasmonate-induced defenses: a tale of intelligence, collaborators and rascals
  - Trends Pl Sci 16(5):249-257 (2011)
  Plants have sophisticated defense systems to protect their tissues against the attack of herbivorous organisms. Many of these defenses are orchestrated by the oxylipin jasmonate. A growing body of evidence indicates that the expression of jasmonate-induced responses is tightly regulated by the ecological context of the plant. Ecological information is provided by molecular signals that indicate the nature of the attacker, the value of the attacked organs, phytochrome status and thereby proximity of competing plants, association with beneficial organisms and history of plant interactions with pathogens and herbivores. This review discusses recent advances in this field and highlights the need to map the activities of informational modulators to specific control points within our emerging model of jasmonate signaling.
• MicroRNA networks and developmental plasticity in plants
  - Trends Pl Sci 16(5):258-264 (2011)
  Plant microRNAs (miRNAs) are embedded in regulatory networks that coordinate different gene expression programs in support of developmental plasticity. Modification of miRNA-target nodes during evolution might in turn underlie morphological and physiological diversity. A survey of the literature indicates that miRNA-target nodes themselves are organized in networks, and here we discuss some of the developmental traits they control along with possible interactions between miRNA and their targets. Because miRNAs and their interactions are not only at the heart of regulating many aspects of developmental plasticity, but because they also have an inherently quantitative mode of action, they present important targets for biotechnology applications.
• Viral suppressors of RNA silencing
  - Trends Pl Sci 16(5):265-272 (2011)
  The infection and replication of viruses in the host induce diverse mechanisms for combating viral infection. One of the best-studied antiviral defence mechanisms is based on RNA silencing. Consistently, several viral suppressors of RNA silencing (VSRs) have been identified from almost all plant virus genera, which are surprisingly diverse within and across kingdoms, exhibiting no obvious sequence similarities. VSRs efficiently inhibit host antiviral responses by interacting with the key components of cellular silencing machinery, often mimicking their normal cellular functions. Recent findings have revealed that the impact of VSRs on endogenous pathways is more complex and profound than had been estimated thus far. This review highlights the current understanding of and new insights into the mechanisms and functions of plant VSRs.
• Organization and dynamics of plant interphase chromosomes
  - Trends Pl Sci 16(5):273-281 (2011)
  Eukaryotic chromosomes occupy distinct territories within interphase nuclei. The arrangement of chromosome territories (CTs) is important for replication, transcription, repair and recombination processes. Our knowledge about interphase chromatin arrangement is mainly based on results from in situ labeling approaches. The phylogenetic affiliation of a species, cell cycle, differentiation status and environmental factors are all likely to influence interphase nuclear architecture. In this review we survey current data about relative positioning of CTs, somatic pairing of homologs, and sister chromatid alignment in meristematic and differentiated tissues, using data derived mainly from Arabidopsis thaliana, wheat (Triticum aestivum) and their relatives. We discuss morphological constraints and epigenetic impacts on nuclear architecture, the evolutionary stability of CT arrangements, and alterations of nuclear architecture during transcription and repair.
• Fast-forward genetics enabled by new sequencing technologies
  - Trends Pl Sci 16(5):282-288 (2011)
  New sequencing technologies are dramatically accelerating progress in forward genetics, and the use of such methods for the rapid identification of mutant alleles will be soon routine in many laboratories. A straightforward extension will be the cloning of major-effect genetic variants in crop species. In the near future, it can be expected that mapping by sequencing will become a centerpiece in efforts to discover the genes responsible for quantitative trait loci. The largest impact, however, might come from the use of these strategies to extract genes from non-model, non-crop plants that exhibit heritable variation in important traits. Deployment of such genes to improve crops or engineer microbes that produce valuable compounds heralds a potential paradigm shift for plant biology.