The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle.

The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Here we select Spirodela polyrhiza for whole-genome sequencing. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. Its genome has only 19,623 predicted protein-coding genes, which is 28% less than the dicotyledonous Arabidopsis thaliana and 50% less than monocotyledonous rice. We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and will be instrumental for future bioenergy applications.

Diffusion within ultrathin, dense nanoporous silica films.

In this work the origin of permselectivity in dense silica films which possess a pore structure with pore sizes commensurate with the molecular size of the diffusing gas species is investigated. Much of the recently reported work in this field has involved the development of composite membrane films, and while it is generally assumed that the transport process of the gas species within the selective layer of these films is activated in nature, there are anomalies with this simplified picture. In this paper a new model is developed which, for the first time, explains the permselective behavior of the thin selective coatings ubiquitous to membrane separation processes. The model involves the existence of two primary transport domains within the solid film, one of which rapidly conducts the permeating gas (under non-Fickian conditions), while the second domain involves a slow diffusion mode characterized by normal Fickian transport. To validate the model, molecular dynamics simulations are conducted for diffusion of a number of simple gases (He, N(2), and CO(2)) within silica glasses over a range of solid densities. The silica media employed in these studies are based on a novel approach developed in this work for the construction of three-dimensionally periodic atomistic structures of silica of arbitrary density in which network bond connectivity is ensured. The results obtained from this work are in qualitative agreement with experimental observations and confirm the existence of dual mode transport which is central to the interpretation of the permselectivity in composite membranes systems.

Novel, nanoporous silica and titania layers fabricated by magnetron sputtering.

Composite asymmetric membranes are fabricated through the deposition of submicrometer thick (100 nm) silica (SiO(2)) and titania (TiO(2)) films onto flat nanoporous silica and zirconia substrates by magnetron sputtering. The deposition conditions for both coating types were systematically altered to determine their influence on the deposited coating morphology and thickness. Ideal He/N(2) gas selectivity was measured for all of the membranes. The TiO(2) coatings, when deposited onto a ZrO(2) support layer with a pore size of 3 nm, formed a long columnar grain structure with average column diameter of 38 nm. A similar columnar structure was observed for TiO(2) coatings deposited onto a SiO(2) support layer with a pore size of 1 nm. Under the same conditions, SiO(2) coatings, deposited onto the same SiO(2) supports, formed a closely packed spherical grain structure whereas, when deposited onto ZrO(2) supports, the SiO(2) coatings formed an open grain structure. The average SiO(2) grain diameter was 36 nm in both cases. This preliminary investigation was aimed at studying the effect of sputtering parameters on the density and morphology of the deposited coatings. For the depositions carried out, the coating material was found to be very dense. However, the presence of grain boundaries resulted in poor ideal He/N(2) separation efficiencies.

The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.

The DIURNAL project ( http://diurnal.cgrb.oregonstate.edu/ ) provides a graphical interface for mining and viewing diurnal and circadian microarray data for Arabidopsis thaliana, poplar, and rice. The database is searchable and provides access to several user-friendly Web-based data-mining tools with easy-to-understand output. The associated tools include HAYSTACK ( http://haystack.cgrb.oregonstate.edu/ ) and ELEMENT ( http://element.cgrb.oregonstate.edu/ ). HAYSTACK is a model-based pattern-matching algorithm for identifying genes that are coexpressed and potentially coregulated. HAYSTACK can be used to analyze virtually any large-scale microarray data set and provides an alternative method for clustering microarray data from any experimental system by grouping together genes whose expression patterns match the same or similar user-defined patterns. ELEMENT is a Web-based program for identifying potential cis-regulatory elements in the promoters of coregulated genes in Arabidopsis, poplar, and rice. Together, DIURNAL, HAYSTACK, and ELEMENT can be used to facilitate cross-species comparisons among the plant species supported and to accelerate functional genomics efforts in the laboratory.