Improving the statistical preparation for measuring soil N2O flux by closed chamber

Nitrous oxide emissions from soil are known to be spatially and temporally volatile. Reliable estimation of emissions over a given time and space depends on measuring with sufficient intensity but deciding on the number of measuring stations and the frequency of observation can be vexing. The question of low frequency manual observations providing comparable results to high frequency automated sampling also arises. Data collected from a replicated field experiment was intensively studied with the intention to give some statistically robust guidance on these issues. The experiment had nitrous oxide soil to air flux monitored within 10 m by 2.5 m plots by automated closed chambers under a 3 h average sampling interval and by manual static chambers under a three day average sampling interval over sixty days. Observed trends in flux over time by the static chambers were mostly within the auto chamber bounds of experimental error. Cumulated nitrous oxide emissions as measured by each system were also within error bounds. Under the temporal response pattern in this experiment, no significant loss of information was observed after culling the data to simulate results under various low frequency scenarios. Within the confines of this experiment observations from the manual chambers were not spatially correlated above distances of 1 m. Statistical power was therefore found to improve due to increased replicates per treatment or chambers per replicate. Careful after action review of experimental data can deliver savings for future work.

Inhibition of platelet aggregation and 5-HT release by extracts of Australian plants used traditionally as headache treatments

To identify potential migraine therapeutics, extracts of eighteen plants were screened to detect plant constituents affecting ADP induced platelet aggregation and [14C]5-hydroxytryptamine (5-HT) release. Extracts of the seven plants exhibiting significant inhibition of platelet function were reanalysed in the presence of polyvinyl pyrrolidone (PVP) to remove polyphenolic tannins that precipitate proteins. Two of these extracts no longer exhibited inhibition of platelet activity after removal of tannins. However, extracts of Crataegus monogyna, Ipomoea pes-caprae, Eremophila freelingii, Eremophila longifolia, and Asteromyrtus symphyocarpa still potently inhibited ADP induced human platelet [14C]5-HT release in vitro, with levels ranging from 62 to 95% inhibition. I. pes-caprae, and C. monogyna also caused significant inhibition of ADP induced platelet aggregation. All of these plants have been previously used as traditional headache treatments, except for C. monogyna which is used primarily for protective effects on the cardiovascular system. Further studies elucidating the compounds that are responsible for these anti-platelet effects are needed to determine their exact mechanism of action.

Mussel-inspired bioceramics with self-assembled Ca-P/polydopamine composite nanolayer : preparation, formation mechanism, improved cellular bioactivity and osteogenic differentiation of bone marrow stromal cells

The nanostructured surface of biomaterials plays an important role in improving their in vitro cellular bioactivity as well as stimulating in vivo tissue regeneration. Inspired by the mussel’s adhesive versatility, which is thought to be due to the plaque–substrate interface being rich in 3,4-dihydroxy-L-phenylalamine (DOPA) and lysine amino acids, in this study we developed a self-assembly method to prepare a uniform calcium phosphate (Ca-P)/polydopamine composite nanolayer on the surface of b-tricalcium phosphate (b-TCP) bioceramics by soaking b-TCP bioceramics in Tris–dopamine solution. It was found that the addition of dopamine, reaction temperature and reaction time are three key factors inducing the formation of a uniform Ca-P/polydopamine composite nanolayer. The formation mechanism of a Ca-P/polydopamine composite nanolayer involved two important steps: (i) the addition of dopamine to Tris–HCl solution decreases the pH value and accelerates Ca and P ionic dissolution from the crystal boundaries of b-TCP ceramics; (ii) dopamine is polymerized to form self-assembled polydopamine film and, at the same time, nanosized Ca-P particles are mineralized with the assistance of polydopamine, in which the formation of polydopamine occurs simultaneously with Ca-P mineralization (formation of nanosized microparticles composed of calcium phosphate-based materials), and finally a self-assembled Ca-P/polydopamine composite nanolayer forms on the surface of the b-TCP ceramics. Furthermore, the formed self-assembled Ca-P/polydopamine composite nanolayer significantly enhances the surface roughness and hydrophilicity of b-TCP ceramics, and stimulates the attachment, proliferation, alkaline phosphate (ALP) activity and bone-related gene expression (ALP, OCN, COL1 and Runx2) of human bone marrow stromal cells. Our results suggest that the preparation of self-assembled Ca-P/polydopamine composite nanolayers is a viable method to modify the surface of biomaterials by significantly improving their surface physicochemical properties and cellular bioactivity for bone regeneration application.

Preparation of metal-TCNQ charge-transfer complexes on conducting and insulating surfaces by photocrystallization

A generic method for the synthesis of metal-7,7,8,8-tetracyanoquinodimethane (TCNQ) charge-transfer complexes on both conducting and nonconducting substrates is achieved by photoexcitation of TCNQ in acetonitrile in the presence of a sacrificial electron donor and the relevant metal cation. The photochemical reaction leads to reduction of TCNQ to the TCNQ- monoanion. In the presence of Mx+(MeCN), reaction with TCNQ-(MeCN) leads to deposition of Mx+[TCNQ]x crystals onto a solid substrate with morphologies that are dependent on the metal cation. Thus, CuTCNQ phase I photocrystallizes as uniform microrods, KTCNQ as microrods with a random size distribution, AgTCNQ as very long nanowires up to 30 μm in length and with diameters of less than 180 nm, and Co[TCNQ]2(H2O)2 as nanorods and wires. The described charge-transfer complexes have been characterized by optical and scanning electron microscopy and IR and Raman spectroscopy. The CuTCNQ and AgTCNQ complexes are of particular interest for use in memory storage and switching devices. In principle, this simple technique can be employed to generate all classes of metal−TCNQ complexes and opens up the possibility to pattern them in a controlled manner on any type of substrate.

Using strategically applied grazing to manage invasive alien plants in novel grasslands

Introduction Novel ecosystems that contain new combinations of invasive alien plants (IAPs) present a challenge for managers. Yet, control strategies that focus on the removal of the invasive species and/or restoring historical disturbance regimes often do not provide the best outcome for long-term control of IAPs and the promotion of more desirable plant species. Methods This study seeks to identify the primary drivers of grassland invasion to then inform management practices toward the restoration of native ecosystems. By revisiting both published and unpublished data from experiments and case studies within mainly an Australian context for native grassland management, we show how alternative states models can help to design control strategies to manage undesirable IAPs by manipulating grazing pressure. Results Ungulate grazing is generally considered antithetical to invasive species management because in many countries where livestock production is a relatively new disturbance to grasslands (such as in Australia and New Zealand as well as Canada and the USA), selective grazing pressure may have facilitated opportunities for IAPs to establish. We find that grazing stock can be used to manipulate species composition in favour of the desirable components in pastures, but whether grazing is rested or strategically applied depends on the management goal, sizes of populations of the IAP and more desirable species, and climatic and edaphic conditions. Conclusions Based on our findings, we integrated these relationships to develop a testable framework for managing IAPs with strategic grazing that considers both the current state of the plant community and the desired future state—i.e. the application of the principles behind reclamation, rehabilitation, restoration or all three—over time.

‘We’ve always cooked kangaroo. We still cook kangaroo. Although sometimes we use cookbooks now’ : Aboriginal Australians and cookbooks

Aboriginal Australians have a long history of eating native animals and plants. Food preparation techniques were handed down through the generations, without any need for cookbooks. But colonisation changed the diets of Aboriginal Australians, introducing us to a processed diet high in salt, sugar and fat, and causing a wide range of diet-related health problems. Over the years, many Aboriginal Australians lost their connections to traditional food preparation practices. In this paper, the authors provide a brief overview of Aboriginal food history and describe a newly-emerging focus on reintroducing native foods. They describe the work of an Aboriginal chef, Dale Chapman, who is actively promoting native foods and creating a native-Western food fusion. Chapman has developed native food recipes and a cookbook, in an effort to make native foods accessible to all Australians. She promotes a future when native foods are part of the identity of all Australians – both Aboriginal and non-Aboriginal.

Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA

Many examples of extreme virus resistance and posttranscriptional gene silencing of endogenous or reporter genes have been described in transgenic plants containing sense or antisense transgenes. In these cases of either cosuppression or antisense suppression, there appears to be induction of a surveillance system within the plant that specifically degrades both the transgene and target RNAs. We show that transforming plants with virus or reporter gene constructs that produce RNAs capable of duplex formation confer virus immunity or gene silencing on the plants. This was accomplished by using transcripts from one sense gene and one antisense gene colocated in the plant genome, a single transcript that has self-complementarity, or sense and antisense transcripts from genes brought together by crossing. A model is presented that is consistent with our data and those of other workers, describing the processes of induction and execution of posttranscriptional gene silencing.

Hairpin RNAs derived from RNA polymerase II and polymerase III promoter-directed transgenes are processed differently in plants

RNA polymerase III (Pol III) as well as Pol II (35S) promoters are able to drive hairpin RNA (hpRNA) expression and induce target gene silencing in plants. siRNAs of 21 nt are the predominant species in a 35S Pol II line, whereas 24- and/or 22-nucleotide (nt) siRNAs are produced by a Pol III line. The 35S line accumulated the loop of the hpRNA, in contrast to full-length hpRNA in the Pol III line. These suggest that Pol II and Pol III-transcribed hpRNAs are processed by different pathways. One Pol III transgene produced only 24-nt siRNAs but silenced the target gene efficiently, indicating that the 24-nt siRNAs can direct mRNA degradation; specific cleavage was confirmed by 59 rapid amplification of cDNA ends (RACE). Both Pol II- and Pol III-directed hpRNA transgenes induced cytosine methylation in the target DNA. The extent of methylation is not correlated with the level of 21-nt siRNAs, suggesting that they are not effective inducers of DNA methylation. The promoter of a U6 transgene was significantly methylated, whereas the promoter of the endogenous U6 gene was almost free of cytosine methylation, suggesting that endogenous sequences are more resistant to de novo DNA methylation than are transgene constructs. Published by Cold Spring Harbor Laboratory Press. Copyright © 2008 RNA Society.

Replicating satellite RNA induces sequence-specific DNA methylation and truncated transcripts in plants

Tobacco plants were transformed with a chimeric transgene comprising sequences encoding β-glucuronidase (GUS) and the satellite RNA (satRNA) of cereal yellow dwarf luteovirus. When transgenic plants were infected with potato leafroll luteovirus (PLRV), which replicated the transgene-derived satRNA to a high level, the satellite sequence of the GUS:Sat transgene became densely methylated. Within the satellite region, all 86 cytosines in the upper strand and 73 of the 75 cytosines in the lower strand were either partially or fully methylated. In contrast, very low levels of DNA methylation were detected in the satellite sequence of the transgene in uninfected plants and in the flanking nonsatellite sequences in both infected and uninfected plants. Substantial amounts of truncated GUS:Sat RNA accumulated in the satRNA-replicating plants, and most of the molecules terminated at nucleotides within the first 60 bp of the satellite sequence. Whereas this RNA truncation was associated with high levels of satRNA replication, it appeared to be independent of the levels of DNA methylation in the satellite sequence, suggesting that it is not caused by methylation. All the sequenced GUS:Sat DNA molecules were hypermethylated in plants with replicating satRNA despite the phloem restriction of the helper PLRV. Also, small, sense and antisense ∼22 nt RNAs, derived from the satRNA, were associated with the replicating satellite. These results suggest that the sequence-specific DNA methylation spread into cells in which no satRNA replication occurred and that this was mediated by the spread of unamplified satRNA and/or its associated 22 nt RNA molecules.

RNA interference-inducing hairpin RNAs in plants act through the viral defence pathway

RNA interference (RNAi) is widely used to silence genes in plants and animals. It operates through the degradation of target mRNA by endonuclease complexes guided by approximately 21 nucleotide (nt) short interfering RNAs (siRNAs). A similar process regulates the expression of some developmental genes through approximately 21 nt microRNAs. Plants have four types of Dicer-like (DCL) enzyme, each producing small RNAs with different functions. Here, we show that DCL2, DCL3 and DCL4 in Arabidopsis process both replicating viral RNAs and RNAi-inducing hairpin RNAs (hpRNAs) into 22-, 24- and 21 nt siRNAs, respectively, and that loss of both DCL2 and DCL4 activities is required to negate RNAi and to release the plant's repression of viral replication. We also show that hpRNAs, similar to viral infection, can engender long-distance silencing signals and that hpRNA-induced silencing is suppressed by the expression of a virus-derived suppressor protein. These findings indicate that hpRNA-mediated RNAi in plants operates through the viral defence pathway.

RNA silencing in plants: Yesterday, today, and tomorrow

RNA silencing has become a major focus of molecular biology and biomedical research around the world. This is highlighted by a simple PubMed search for “RNA silencing,” which retrieves almost 9,000 articles. Interest in gene silencing-related mechanisms stemmed from the early 1990s, when this phenomenon was first noted as a surprise observation by plant scientists during the course of plant transformation experiments, in which the introduction of a transgene into the genome led to the silencing of both the transgene and homologous endogenes. From these initial studies, plant biologists have continued to generate a wealth of information into not only gene silencing mechanisms but also the complexity of these biological pathways as well as revealing their multilevel interactions with one another. The plant biology community has also made significant advancements in exploiting RNA silencing as a powerful tool for gene function studies and crop improvements. In this article, we (1) review the rich history of gene silencing research and the knowledge it has generated into our understanding of this fundamental mechanism of gene regulation in plants; (2) describe examples of the current applications of RNA silencing in crop plants; and (3) discuss improvements in RNA silencing technology and its potential application in plant science.

The RNA world in plants: Post-transcriptional control III

Post-transcriptional control of gene expression has gone from a curiosity involving a few special genes to a highly diverse and widespread set of processes that is truly pervasive in plant gene expression. Thus, Plant Cell readers interested in almost any aspect of plant gene expression in response to any environmental influence, or in development, are advised to read on. In May 2001, what has become the de facto third biennial Symposium on Post-Transcriptional Control of Gene Expression in Plants was held in Ames, Iowa. The meeting was hosted by the new Plant Sciences Institute of Iowa State University with additional funding from the National Science Foundation and the United States Department of Agriculture. In 1997, the annual University of California-Riverside Plant Physiology Symposium was devoted to this topic. This provided a wake-up call to the plant world, summarized in this journal (Gallie and Bailey-Serres, 1997), that not all gene expression is controlled at the level of transcription. This was expanded upon at a European Molecular Biology Organization Workshop in Leysin, Switzerland, in 1999 (Bailey-Serres et al., 1999). The 3-day meeting in Ames brought together a strong and diverse contingent of plant biologists from four continents. The participants represented an unusually heterogeneous group of disciplines ranging from virology to stress response to computational biology. The research approaches and techniques represented were similarly diverse. Here we discuss a sample of the many fascinating aspects of post-transcriptional control that were presented at this meeting; we apologize to those whose work is not described here.

RNAi for insect-proof plants

RNA interference induced in insects after ingestion of plant-expressed hairpin RNA offers promise for managing devastating crop pests

Small RNA viruses of insects : expression in plants and RNA silencing

Interest in insect small RNA viruses (SRVs) has grown slowly but steadily. A number of new viruses have been analyzed at the sequence level, adding to our knowledge of their diversity at the level of both individual virus species and families. In particular, a number of possible new virus families have emerged. This research has largely been driven by interest in their potential for pest control, as well as in their importance as the causal agents of disease in beneficial arthropods. At the same time, research into known viruses has made valuable contributions to our understanding of an emerging new field of central importance to molecular biology-the existence of RNA-based gene silencing, developmental control, and adaptive immune systems in eukaryotes. Subject to RNA-based adaptive immune responses in their hosts, viruses have evolved a variety of genes encoding proteins capable of suppressing the immune response. Such genes were first identified in plant viruses, but the first examples known from animal viruses were identified in insect RNA viruses. This chapter will address the diversity of insect SRVs, and attempts to harness their simplicity in the engineering of transgenic plants expressing viruses for resistance to insect pests. We also describe RNA interference and antiviral pathways identified in plants and animals, how they have led viruses to evolve genes capable of suppressing such adaptive immunity, and the problems presented by these pathways for the strategy of expressing viruses in transgenic plants. Approaches for countering these problems are also discussed. © 2006 Elsevier Inc. All rights reserved.