Plant biology: Coding in non-coding RNAs

The discovery of peptides encoded by what were thought to be non-coding – or 'junk' – regions of precursors to microRNA sequences reveals a new layer of gene regulation. These sequences may not be junk, after all.

Franklin Barley: Patent law and plant breeders’ rights

This paper considers the relationship between patent law and plant breeders' rights in light of modern developments in biotechnology. It examines how a number of superior courts have sought to manage the tensions and conflicts between these competing schemes of intellectual property protection. Part 1 considers the High Court of Australia case of Grain Pool of Western Australia v the Commonwealth dealing with Franklin barley. Part 2 examines the significance of the Supreme Court of the United States decision in JEM Ag Supply Inc v Pioneer Hi-Bred International Inc with respect to utility patents and hybrid seed. Part 3 considers the Supreme Court of Canada case of Harvard College v the Commissioner of Patents dealing with the transgenic animal, oncomouse, and discusses its implications for the forthcoming appeal from the Federal Court case of Percy Schmeiser v Monsanto.

Substrate effects in the supramolecular assembly of 1,3,5-benzene tricarboxylic acid on graphite and graphene

The behavior of small molecules on a surface depends critically on both molecule–substrate and intermolecular interactions. We present here a detailed comparative investigation of 1,3,5-benzene tricarboxylic acid (trimesic acid, TMA) on two different surfaces: highly oriented pyrolytic graphite (HOPG) and single-layer graphene (SLG) grown on a polycrystalline Cu foil. On the basis of high-resolution scanning tunnelling microscopy (STM) images, we show that the epitaxy matrix for the hexagonal TMA chicken wire phase is identical on these two surfaces, and, using density functional theory (DFT) with a non-local van der Waals correlation contribution, we identify the most energetically favorable adsorption geometries. Simulated STM images based on these calculations suggest that the TMA lattice can stably adsorb on sites other than those identified to maximize binding interactions with the substrate. This is consistent with our net energy calculations that suggest that intermolecular interactions (TMA–TMA dimer bonding) are dominant over TMA–substrate interactions in stabilizing the system. STM images demonstrate the robustness of the TMA films on SLG, where the molecular network extends across the variable topography of the SLG substrates and remains intact after rinsing and drying the films. These results help to elucidate molecular behavior on SLG and suggest significant similarities between adsorption on HOPG and SLG.

Plant species’ origin predicts dominance and response to nutrient enrichment and herbivores in global grasslands

Exotic species dominate many communities; however the functional significance of species’ biogeographic origin remains highly contentious. This debate is fuelled in part by the lack of globally replicated, systematic data assessing the relationship between species provenance, function and response to perturbations. We examined the abundance of native and exotic plant species at 64 grasslands in 13 countries, and at a subset of the sites we experimentally tested native and exotic species responses to two fundamental drivers of invasion, mineral nutrient supplies and vertebrate herbivory. Exotic species are six times more likely to dominate communities than native species. Furthermore, while experimental nutrient addition increases the cover and richness of exotic species, nutrients decrease native diversity and cover. Native and exotic species also differ in their response to vertebrate consumer exclusion. These results suggest that species origin has functional significance, and that eutrophication will lead to increased exotic dominance in grasslands.

Plant Breeder's Rights: An Australian commentary December 2004

The aim of this manual is to provide a practical guide to the Plant Breeder's Rights Act 1994 (Cth). It is a resource of information about the legislation, its administration, and its operation. This commentary is intended to assist plant breeders, scientific researchers, and business managers who want to make a more effective use of the Plant Breeder's Rights Act 1994 (Cth) in the management and commercialisation of their intellectual property rights. It is also designed to enhance the understanding of the legislation among lawyers, patent attorneys, qualified persons, and policy-makers.

Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana

Background Nicotiana benthamiana is an allo-tetraploid plant, which can be challenging for de novo transcriptome assemblies due to homeologous and duplicated gene copies. Transcripts generated from such genes can be distinct yet highly similar in sequence, with markedly differing expression levels. This can lead to unassembled, partially assembled or mis-assembled contigs. Due to the different properties of de novo assemblers, no one assembler with any one given parameter space can re-assemble all possible transcripts from a transcriptome. Results In an effort to maximise the diversity and completeness of de novo assembled transcripts, we utilised four de novo transcriptome assemblers, TransAbyss, Trinity, SOAPdenovo-Trans, and Oases, using a range of k-mer sizes and different input RNA-seq read counts. We complemented the parameter space biologically by using RNA from 10 plant tissues. We then combined the output of all assemblies into a large super-set of sequences. Using a method from the EvidentialGene pipeline, the combined assembly was reduced from 9.9 million de novo assembled transcripts to about 235,000 of which about 50,000 were classified as primary. Metrics such as average bit-scores, feature response curves and the ability to distinguish paralogous or homeologous transcripts, indicated that the EvidentialGene processed assembly was of high quality. Of 35 RNA silencing gene transcripts, 34 were identified as assembled to full length, whereas in a previous assembly using only one assembler, 9 of these were partially assembled. Conclusions To achieve a high quality transcriptome, it is advantageous to implement and combine the output from as many different de novo assemblers as possible. We have in essence taking the ‘best’ output from each assembler while minimising sequence redundancy. We have also shown that simultaneous assessment of a variety of metrics, not just focused on contig length, is necessary to gauge the quality of assemblies.

Development of multi-rotor localised surveillance using multi-spectral sensors for plant biosecurity

This report describes a proof of concept for multi-rotor localised surveillance using a multi-spectral sensor for plant biosecurity applications. A literature review was conducted on previous applications using airborne multispectral imaging for plant biosecurity purposes. A ready built platform was purchased and modified in order to fit and provide suitable clearance for a Tetracam Mini-MCA multispectral camera. The appropriate risk management documents were developed allowing the platform and the multi-spectral camera to be tested extensively. However, due to technical difficulties with the platform the Mini- MCA was not mounted to the platform. Once a suitable platform is developed, future extensions can be conducted into the suitability of the Mini-MCA for airborne surveillance of Australian crops.

Cytotoxic C20 diterpenoid alkaloids from the Australian endemic rainforest plant Anopterus macleayanus

In order to identify new anticancer compounds from nature, a prefractionated library derived from Australian endemic plants was generated and screened against the prostate cancer cell line LNCaP using a metabolic assay. Fractions from the seeds, leaves, and wood of Anopterus macleayanus showed cytotoxic activity and were subsequently investigated using a combination of bioassay-guided fractionation and mass-directed isolation. This led to the identification of four new diterpenoid alkaloids, 6α-acetoxyanopterine (1), 4′-hydroxy-6α-acetoxyanopterine (2), 4′-hydroxyanopterine (3), and 11α-benzoylanopterine (4), along with four known compounds, anopterine (5), 7β-hydroxyanopterine (6), 7β,4′-dihydroxyanopterine (7), and 7β-hydroxy-11α-benzoylanopterine (8); all compounds were purified as their trifluoroacetate salt. The chemical structures of 1–8 were elucidated after analysis of 1D/2D NMR and MS data. Compounds 1–8 were evaluated for cytotoxic activity against a panel of human prostate cancer cells (LNCaP, C4-2B, and DuCaP) and nonmalignant cell lines (BPH-1 and WPMY-1), using a live-cell imaging system and a metabolic assay. All compounds showed potent cytotoxicity with IC50 values of <400 nM; compound 1 was the most active natural product from this series, with an IC50 value of 3.1 nM toward the LNCaP cell line. The live-cell imaging assay on 1–8 showed a concentration- and time-dependent effect on the cell morphology and proliferation of LNCaP cells.

Reply to comment on 'Bi nanolines on Si(001): Registry with the substrate'

The registry of bismuth dimers, integral components of the bismuth nanoline on Si(001), is examined. In contrast to the currently accepted view, the bismuth dimers are found to be in registry with the two-dimensional lattice created by the silicon dimers. The consequences of this finding are briefly explored.

Substrate, molecular structure, and solvent effects in 2D self-assembly via hydrogen and halogen bonding

Recently, halogen···halogen interactions have been demonstrated to stabilize two-dimensional supramolecular assemblies at the liquid–solid interface. Here we study the effect of changing the halogen, and report on the 2D supramolecular structures obtained by the adsorption of 2,4,6-tris(4-bromophenyl)-1,3,5-triazine (TBPT) and 2,4,6-tris(4-iodophenyl)-1,3,5-triazine (TIPT) on both highly oriented pyrolytic graphite and the (111) facet of a gold single crystal. These molecular systems were investigated by combining room-temperature scanning tunneling microscopy in ambient conditions with density functional theory, and are compared to results reported in the literature for the similar molecules 1,3,5-tri(4-bromophenyl)benzene (TBPB) and 1,3,5-tri(4-iodophenyl)benzene (TIPB). We find that the substrate exerts a much stronger effect than the nature of the halogen atoms in the molecular building blocks. Our results indicate that the triazine core, which renders TBPT and TIPT stiff and planar, leads to stronger adsorption energies and hence structures that are different from those found for TBPB and TIPB. On the reconstructed Au(111) surface we find that the TBPT network is sensitive to the fcc- and hcp-stacked regions, indicating a significant substrate effect. This makes TBPT the first molecule reported to form a continuous monolayer at room temperature in which molecular packing is altered on the differently reconstructed regions of the Au(111) surface. Solvent-dependent polymorphs with solvent coadsorption were observed for TBPT on HOPG. This is the first example of a multicomponent self-assembled molecular networks involving the rare cyclic, hydrogen-bonded hexamer of carboxylic groups, R66(24) synthon.

Gene patent practice across plant and human genomes

The uses of genetic sequences to inform, enable or create products or services for human biomedicine are substantially different from their uses in crop-based agriculture. Here, we explore what similarities and differences may emerge in patent use and strategies, and map patent-disclosed sequences onto three important plant genomes: maize (corn), rice and soybean. We focus on those referenced in the granted patent claims to compare their uses to the approach used in human gene patenting.

The ownership question of plant gene and genome intellectual properties

The restructuring of the crop agriculture industry over the past two decades has enabled patent holders to exclude, prevent and deter others from using certain research tools and delay or block further follow-on inventions

A multiscale study on the structural and mechanical properties of the luffa sponge from Luffa cylindrica plant

Cellular materials that are often observed in biological systems exhibit excellent mechanical properties at remarkably low densities. Luffa sponge is one of such materials with a complex interconnecting porous structure. In this paper, we studied the relationship between its structural and mechanical properties at different levels of its hierarchical organization from a single fiber to a segment of whole sponge. The tensile mechanical behaviors of three single fibers were examined by an Instron testing machine and the ultrastructure of a fractured single fiber was observed in a scanning electronic microscope. Moreover, the compressive mechanical behaviors of the foam-like blocks from different locations of the sponge were examined. The difference of the compressive stress-strain responses of four sets of segmental samples were also compared. The result shows that the single fiber is a porous composite material mainly consisting of cellulose fibrils and lignin/hemicellulose matrix, and its Young's modulus and strength are comparable to wood. The mechanical behavior of the block samples from the hoop wall is superior to that from the core part. Furthermore, it shows that the influence of the inner surface on the mechanical property of the segmental sample is stronger than that of the core part; in particular, the former's Young's modulus, strength and strain energy absorbed are about 1.6 times higher. The present work can improve our understanding of the structure-function relationship of the natural material, which may inspire fabrication of new biomimetic foams with desirable mechanical efficiency for further applications in anti-crushing devices and super-light sandwich panels.

Plant height affects Fusarium crown rot severity in wheat

Effects of plant height on Fusarium crown rot (FCR) disease severity were investigated using 12 pairs of near-isogenic lines (NILs) for six different reduced height (Rht) genes in wheat. The dwarf isolines all gave better FCR resistance when compared with their respective tall counterparts, although the Rht genes involved in these NILs are located on several different chromosomes. Treating plants with exogenous gibberellin increased FCR severity as well as seedling lengths in all of the isolines tested. Analysis of the expression of several defense genes with known correlation with resistance to FCR pathogens between the Rht isolines following FCR inoculation indicated that the better resistance of the dwarf isolines was not due to enhanced defense gene induction. These results suggested that the difference in FCR severity between the tall and dwarf isolines is likely due to their height difference per se or to some physiological and structural consequences of reduced height. Thus, caution should be taken when considering to exploit any FCR locus located near a height gene.

Organosolv pretreatment of plant biomass for enhanced enzymatic saccharification

The combination of dwindling petroleum reserves and population growth make the development of renewable energy and chemical resources more pressing than ever before. Plant biomass is the most abundant renewable source for energy and chemicals. Enzymes can selectively convert the polysaccharides in plant biomass into simple sugars which can then be upgraded to liquid fuels and platform chemicals using biological and/or chemical processes. Pretreatment is essential for efficient enzymatic saccharification of plant biomass and this article provides an overview of how organic solvent (organosolv) pretreatments affect the structure and chemistry of plant biomass, and how these changes enhance enzymatic saccharification. A comparison between organosolv pretreatments utilizing broadly different classes of solvents (i.e., low boiling point, high boiling point, and biphasic) is presented, with a focus on solvent recovery and formation of by-products. The reaction mechanisms that give rise to these by-products are investigated and strategies to minimize by-product formation are suggested. Finally, process simulations of organosolv pretreatments are compared and contrasted, and discussed in the context of an industrial-scale plant biomass to fermentable sugar process.