Application of gene silencing in plants

Recent studies of gene silencing in plants have revealed two RNA-mediated epigenetic processes, RNA-directed RNA degradation and RNA-directed DNA methylation. These natural processes have provided new avenues for developing high-efficiency, high-throughput technology for gene suppression in plants.

RNA Silencing in Plants

RNA silencing-related mechanisms have been documented in almost all living organisms and RNA silencing is now used as board term to describe the vast array of related processes involving RNA–RNA, RNA–DNA, RNA–protein or protein–protein interactions that ultimately result in the repression of gene expression. In plants, the parallel RNA silencing pathways have evolved to extraordinary levels of complexity and diversity, playing crucial roles in providing protection against invading nucleic acids derived from viruses or replicating transposons, controlling chromatin modifications as well as regulating endogenous gene expression to ensure normal plant growth and development. The aims of this chapter are (1) to provide an overview of the initial curious observations of RNA silencing-related phenomena in plants, (2) to outline the parallel gene silencing pathways of plants, and (3) to discuss current applications of RNA silencing technologies to not only study but also modify plant development

High-throughput vectors for efficient gene silencing in plants

A major challenge in the post-genome era of plant biology is to determine the functions of all genes in the plant genome. A straightforward approach to this problem is to reduce or knockout expression of a gene with the hope of seeing a phenotype that is suggestive of its function. Insertional mutagenesis is a useful tool for this type of study but is limited by gene redundancy, lethal knockouts, non-tagged mutants, and the inability to target the inserted element to a specific gene. The efficacy of gene silencing in plants using inverted-repeat transgene constructs that encode a hairpin RNA (hpRNA) has been demonstrated by a number of groups, and has several advantages over insertional mutagenesis. In this paper we describe two improved pHellsgate vectors that facilitate rapid generation of hpRNA-encoding constructs, pHellsgate 4 allows the production of an hpRNA construct in a single step from a single polymerase chain reaction product, while pHellsgate 8 requires a two-step process via an intermediate vector. We show that these vectors are effective at silencing three endogenous genes in Arabidopsis, FLOWERING LOCUS C, PHYTOENE DESATURASE and ETHYLENE INSENSITIVE 2. We also show that a construct of sequences from two genes silences both genes.

Construct design for efficient, effective and high-throughput gene silencing in plants

Post-transcriptional silencing of plant genes using anti-sense or co-suppression constructs usually results in only a modest proportion of silenced individuals. Recent work has demonstrated the potential for constructs encoding self-complementary 'hairpin' RNA (hpRNA) to efficiently silence genes. In this study we examine design rules for efficient gene silencing, in terms of both the proportion of independent transgenic plants showing silencing, and the degree of silencing. Using hpRNA constructs containing sense/anti-sense arms ranging from 98 to 853 nt gave efficient silencing in a wide range of plant species, and inclusion of an intron in these constructs had a consistently enhancing effect. Intron-containing constructs (ihpRNA) generally gave 90-100% of independent transgenic plants showing silencing. The degree of silencing with these constructs was much greater than that obtained using either co-suppression or anti-sense constructs. We have made a generic vector, pHANNIBAL, that allows a simple, single PCR product from a gene of interest to be easily converted into a highly effective ihpRNA silencing construct. We have also created a high-throughput vector, pHELLSGATE, that should facilitate the cloning of gene libraries or large numbers of defined genes, such as those in EST collections, using an in vitro recombinase system. This system may facilitate the large-scale determination and discovery of plant gene functions in the same way as RNAi is being used to examine gene function in Caenorhabditis elegans.

A rapid and simple method of assaying plants transformed with hygromycin or PPT resistance genes

A very simple leaf assay is described that rapidly and reliably identifies transgenic plants expressing the hygromycin resistance gene, hph or the phosphinothricin resistance gene, bar. Leaf tips were cut from plants propagated either in the glasshouse or in tissue culture and the cut surface embedded in solid medium containing the appropriate selective agent. Non-transgenic barley or rice leaf tips had noticeable symptoms of either bleaching or necrosis after three days on the medium and were completely bleached or necrotic after one week. Transgenic leaf tips remained green and healthy over this period. This gave unambiguous discrimination between transgenic and non-transgenic plants. The leaf assay was also effective for dicot plants tested (tobacco and peas).

Expression patterns of vascular-specific promoters RolC and Sh in transgenic potatoes and their use in engineering PLRV-resistant plants

The expression patterns of GUS fusion constructs driven by the Agrobacterium rhizogenes RolC and the maize Sh (Shrunken: sucrose synthase-1) promoters were examined in transgenic potatoes (cv. Atlantic). RolC drove high-level gene expression in phloem tissue, bundle sheath cells and vascular parenchyma, but not in xylem or non-vascular tissues. Sh expression was exclusively confined to phloem tissue. Potato leafroll luteovirus (PLRV) replicates only in phloem tissues, and we show that when RolC is used to drive expression of the PLRV coat protein gene, virus-resistant lines can be obtained. In contrast, no significant resistance was observed when the Sh promoter was used.

Firmicutes dominate the bacterial taxa within sugar-cane processing plants

Sugar cane processing sites are characterised by high sugar/hemicellulose levels, available moisture and warm conditions, and are relatively unexplored unique microbial environments. The PhyloChip microarray was used to investigate bacterial diversity and community composition in three Australian sugar cane processing plants. These ecosystems were highly complex and dominated by four main Phyla, Firmicutes (the most dominant), followed by Proteobacteria, Bacteroidetes, and Chloroflexi. Significant variation (p , 0.05) in community structure occurred between samples collected from ‘floor dump sediment’, ‘cooling tower water’, and ‘bagasse leachate’. Many bacterial Classes contributed to these differences, however most were of low numerical abundance. Separation in community composition was also linked to Classes of Firmicutes, particularly Bacillales, Lactobacillales and Clostridiales, whose dominance is likely to be linked to their physiology as ‘lactic acid bacteria’, capable of fermenting the sugars present. This process may help displace other bacterial taxa, providing a competitive advantage for Firmicutes bacteria.

Experimental verification of the modified spring-mass theory of fiber Bragg grating accelerometers using transverse forces

A fiber Bragg grating (FBG) accelerometer using transverse forces is more sensitive than one using axial forces with the same mass of the inertial object, because a barely stretched FBG fixed at its two ends is much more sensitive to transverse forces than axial ones. The spring-mass theory, with the assumption that the axial force changes little during the vibration, cannot accurately predict its sensitivity and resonant frequency in the gravitational direction because the assumption does not hold due to the fact that the FBG is barely prestretched. It was modified but still required experimental verification due to the limitations in the original experiments, such as the (1) friction between the inertial object and shell; (2) errors involved in estimating the time-domain records; (3) limited data; and (4) large interval ∼5 Hz between the tested frequencies in the frequency-response experiments. The experiments presented here have verified the modified theory by overcoming those limitations. On the frequency responses, it is observed that the optimal condition for simultaneously achieving high sensitivity and resonant frequency is at the infinitesimal prestretch. On the sensitivity at the same frequency, the experimental sensitivities of the FBG accelerometer with a 5.71 gram inertial object at 6 Hz (1.29, 1.19, 0.88, 0.64, and 0.31 nm/g at the 0.03, 0.69, 1.41, 1.93, and 3.16 nm prestretches, respectively) agree with the static sensitivities predicted (1.25, 1.14, 0.83, 0.61, and 0.29 nm/g, correspondingly). On the resonant frequency, (1) its assumption that the resonant frequencies in the forced and free vibrations are similar is experimentally verified; (2) its dependence on the distance between the FBG’s fixed ends is examined, showing it to be independent; (3) the predictions of the spring-mass theory and modified theory are compared with the experimental results, showing that the modified theory predicts more accurately. The modified theory can be used more confidently in guiding its design by predicting its static sensitivity and resonant frequency, and may have applications in other fields for the scenario where the spring-mass theory fails.

Model-predictive control and closed-loop stability considerations for nonlinear plants described by local ARX-type models

In this paper, a model-predictive control (MPC) method is detailed for the control of nonlinear systems with stability considerations. It will be assumed that the plant is described by a local input/output ARX-type model, with the control potentially included in the premise variables, which enables the control of systems that are nonlinear in both the state and control input. Additionally, for the case of set point regulation, a suboptimal controller is derived which has the dual purpose of ensuring stability and enabling finite-iteration termination of the iterative procedure used to solve the nonlinear optimization problem that is used to determine the control signal.

Comparing skin biopsy with confocal microscopy : diagnostic yield of nerve fiber density

Background and aims: The assessment of intra-epidermal nerve fiber density (IENFD) in skin biopsies and corneal nerve fiber density (CNFD) using corneal confocal microscopy (CCM) provides promising techniques to detect small nerve fiber damage in patients with peripheral neuropathy. To help define the clinical utility of each of these techniques in patients with diabetic neuropathy we have assessed sensitivity and specificity of IENFD and CNFD in predicting the following: 1) diabetic polyneuropathy (DPN); 2) risk of foot ulceration (RFU); 3) initial small fiber neuropathy (iSFN); 4) severe small fiber neuropathy (sSFN)...

Design and construction of an in-plant activation cassette for transgene expression and recombinant protein production in plants

Virus-based transgene expression systems have become particularly valuable for recombinant protein production in plants. The dual-module in-plant activation (INPACT) expression platform consists of a uniquely designed split-gene cassette incorporating the cis replication elements of Tobacco yellow dwarf geminivirus (TYDV) and an ethanol-inducible activation cassette encoding the TYDV Rep and RepA replication-associated proteins. The INPACT system is essentially tailored for recombinant protein production in stably transformed plants and provides both inducible and high-level transient transgene expression with the potential to be adapted to diverse crop species. The construction of a novel split-gene cassette, the inducible nature of the system and the ability to amplify transgene expression via rolling-circle replication differentiates this system from other DNA- and RNA-based virus vector systems used for stable or transient recombinant protein production in plants. Here we provide a detailed protocol describing the design and construction of a split-gene INPACT cassette, and we highlight factors that may influence optimal activation and amplification of gene expression in transgenic plants. By using Nicotiana tabacum, the protocol takes 6-9 months to complete, and recombinant proteins expressed using INPACT can accumulate to up to 10% of the leaf total soluble protein.

Mini-scale method for nuclear run-on transcription assay in plants

We present a mini-scale method for nuclear run-on transcription assay. In our method, all the centrifuge steps can be carried out by using micro-tubes for short time (5 min each) throughout the process, including isolation of transcriptionally active nuclei and purification of labeled RNA after synthesis of RNA in isolated nuclei. The assay can be performed using a small amount of plant tissue, which enables analysis of developmental changes in transcriptional status of given genes in a single individual plant. Successful results were obtained using the tissues of flower and leaf of petunia and embryo of pea, suggesting that the method is potentially applicable to a variety of plant tissues.

Transient expression vectors for functional genomics, quantification of promoter activity and RNA silencing in plants

Background We describe novel plasmid vectors for transient gene expression using Agrobacterium, infiltrated into Nicotiana benthamiana leaves. We have generated a series of pGreenII cloning vectors that are ideally suited to transient gene expression, by removing elements of conventional binary vectors necessary for stable transformation such as transformation selection genes. Results We give an example of expression of heme-thiolate P450 to demonstrate effectiveness of this system. We have also designed vectors that take advantage of a dual luciferase assay system to analyse promoter sequences or post-transcriptional regulation of gene expression. We have demonstrated their utility by co-expression of putative transcription factors and the promoter sequence of potential target genes and show how orthologous promoter sequences respond to these genes. Finally, we have constructed a vector that has allowed us to investigate design features of hairpin constructs related to their ability to initiate RNA silencing, and have used these tools to study cis-regulatory effect of intron-containing gene constructs. Conclusion In developing a series of vectors ideally suited to transient expression analysis we have provided a resource that further advances the application of this technology. These minimal vectors are ideally suited to conventional cloning methods and we have used them to demonstrate their flexibility to investigate enzyme activity, transcription regulation and post-transcriptional regulatory processes in transient assays.

Ecological risk analysis of transgenic plants

Public concern about the safety of many forms of industrial technology are known to be linked to a range of factors including a perceived lack of confidence in regulatory decision making.1 The use of transgenic plants in agriculture may be seen as an issue that could generate similar concern. Criticism has been made about the completeness of knowledge on the potential for aberrant behaviour of genetically manipulated organisms (GMO's) in release environments, and the adequacy of existing pre­‐release screening and assessment methodologies (Goldberg & Tjaden, 1990). Such comments are important because any perceived shortcomings in the pre-release assessment of GMO safety may lead to decreased public support of the technology -­‐and the industry itself...

Biaxial fiber Bragg grating accelerometer using axial and transverse forces

We demonstrate the first biaxial fiber Bragg grating (FBG) accelerometer using axial and transverse forces. An inertial object is fixed at the middle of two FBGs inscribed in one fiber. The difference between the resonant wavelengths of the two FBGs can distinguish the acceleration in the axial direction, while being insensitive in the transverse direction. The average of the resonant wavelengths of the two FBGs can distinguish the acceleration in the transverse direction, while being insensitive in the axial direction. In the experiments, when the transverse direction was vertical, the crest-to-trough sensitivity at 5 Hz and resonant frequency of the average were 0.545 nm/g and 34.42 Hz, respectively. When the axial direction was vertical, those of the difference were 0.0454 nm/g and 900 Hz, respectively. For each FBG, the crest-to-trough sensitivity at 5 Hz and resonant frequency in the transverse/vertical direction were 24 and 1/26 times those in the axial/vertical direction, respectively.