RNAi for insect-proof plants

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

Constructs and methods for hairpin RNA-mediated gene silencing in plants

Double-stranded RNA (dsRNA) induces an endogenous sequence-specific RNA degradation mechanism in most eukaryotic cells. The mechanism can be harnessed to silence genes in plants by expressing self-complementary single-stranded (hairpin) RNA in which the duplexed region has the same sequence as part of the target gene's mRNA. We describe a number of plasmid vectors for generating hairpin RNAs, including those designed for high-throughput cloning, and provide protocols for their use.

Efficient silencing of endogenous microRNAs using artificial microRNAs in Arabidopsis thaliana

We report here that the expression of endogenous microRNAs (miRNAs) can be efficiently silenced in Arabidopsis thaliana (Arabidopsis) using artificial miRNA (amiRNA) technology. We demonstrate that an amiRNA designed to target a mature miRNA directs silencing against all miRNA family members, whereas an amiRNA designed to target the stem-loop region of a miRNA precursor transcript directs silencing against only the individual family member targeted. Furthermore, our results indicate that amiRNAs targeting both the mature miRNA and stem-loop sequence direct RNA silencing through cleavage of the miRNA precursor transcript, which presumably occurs in the nucleus of a plant cell during the initial stages of miRNA biogenesis. This suggests that small RNA (sRNA)-guided RNA cleavage in plants occurs not only in the cytoplasm, but also in the nucleus. Many plant miRNA gene families have been identified via sequencing and bioinformatic analysis, but, to date, only a small tranche of these have been functionally characterized due to a lack of effective forward or reverse genetic tools. Our findings therefore provide a new and powerful reverse-genetic tool for the analysis of miRNA function in plants. © The Author 2010. Published by the Molecular Plant Shanghai Editorial Office in association with Oxford University Press on behalf of CSPP and IPPE, SIBS, CAS.

The roles of plant dsRNA-binding proteins in RNAi-like pathways

Dicers are associated with double-stranded RNA-binding proteins (dsRBPs) in animals. In the plant, Arabidopsis, there are four dicer-like (DCL) proteins and five potential dsRBPs. These DCLs act redundantly and hierarchically. However, we show there is little or no redundancy or hierarchy amongst the DRBs in their DCL interactions. DCL1 operates exclusively with DRB1 to produce micro (mi)RNAs, DCL4 operates exclusively with DRB4 to produce trans-acting (ta) siRNAs and 21nt siRNAs from viral RNA. DCL2 and DCL3 produce viral siRNAs without requiring assistance from any dsRBP. DRB2, DRB3 and DRB5 appear unnecessary for mi-, tasi-, viral si-, or heterochromatinising siRNA production but act redundantly in a developmental pathway. © 2008 Federation of European Biochemical Societies.

Cloning and characterization of microRNAs from Brassica napus

A library containing approximately 40,000 small RNA sequences was constructed for Brassica napus. Analysis of 3025 sequences obtained from this library resulted in the identification of 11 conserved miRNA families, which were validated by secondary structure prediction using surrounding sequences in the Brassica genome. Two 21 nt small RNA sequences reside within the arm of a pre-miRNA like stem-loop structure, making them likely candidates for novel non-conserved miRNAs in B. napus. Most of the conserved miRNAs were expressed at similar levels in a F1 hybrid B. napus line and its four double haploid progeny that showed marked variations in phenotypes, but many were differentially expressed between B. napus and Arabidopsis. The miR169 family was expressed at high levels in young leaves and stems, but was undetectable in roots and mature leaves, suggesting that miR169 expression is developmentally regulated in B. napus. © 2007 Federation of European Biochemical Societies.

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.

The genome organization and affinities of an Australian isolate of carrot mottle umbravirus

The genomic sequence of an Australian isolate of carrot mottle umbravirus (CMoV-A) was determined from cDNA generated from dsRNA. This provides the first data on the genome organization and phylogeny of an umbravirus. The 4201-nucleotide genome contains four major open reading frames (ORFs). Analysis suggests that ORF2 encodes an RNA-dependent RNA polymerase, that ORF4 encodes a movement protein, and that the virus has no coat protein gene. The functions of ORFs 1 and 3 remain unknown. ORF2 is probably translated following ribosomal frameshifting. ORFs 3 and 4 are probably translated from a subgenomic mRNA. Sequence comparisons showed CMoV-A to be closely related to pea enation mosaic RNA2 NA2), but also to have affinities with the Bromoviridae. These findings shed light on the relationships between the luteoviruses, PEMV, and the umbraviruses and on the relationships between the carmo-like viruses and the Bromoviridae.

A satellite RNA of barley yellow dwarf virus contains a novel hammerhead structure in the self-cleavage domain

An RNA molecule with properties of a satellite RNA was found in an isolate of barley yellow dwarf virus (BYDV), RPV serotype. It is 322 nucleotides long, single-stranded, and does not hybridize to the viral genome. Dimers of the RNA, which presumably represent replicative intermediates, were able to self-cleave into monomers. In vitro transcripts from cDNA clones were capable of self-cleavage in both the plus (encapsidated) and minus orientations. The sequence flanking the minus strand cleavage site contained a consensus " hammerhead" structure, similar to those found in other self-cleaving satellite RNAs. Although related to the hammerhead structure, sequences flanking the plus strand termini showed differences from the consensus and may be folded into a different structure containing a pseudoknot. © 1991.

Nucleotide sequences of an Australian and a Canadian isolate of potato leafroll luteovirus and their relationships with two European isolates

The genomes of an Australian and a Canadian isolate of potato leafroll virus have been cloned and sequenced. The sequences of both isolates are similar (about 93%), but the Canadian isolate (PLRV-C) is more closely related (about 98% identity) to a Scottish (PLRV-S) and a Dutch isolate (PLRV-N) than to the Australian isolate (PLRV-A). The 5'-terminal 18 nucleotide residues of PLRV-C, PLRV-A, PLRV-N and beet western yellows virus have 17 residues in common. In contrast, PLRV-S shows no obvious similarity in this region. PLRV-A and PLRV-C genomic sequences have localized regions of marked diversity, in particular a 600 nucleotide residue sequence in the polymerase gene. These data provide a world-wide perspective on the molecular biology of PLRV strains and their comparison with other luteoviruses and related RNA plant viruses suggests that there are two major subgroups in the plant luteoviruses.

Tissue viability imaging of skin microcirculation following exposure to whole body cryotherapy (-110°C) and cold water immersion (8°C)

Cryotherapy is currently used in various clinical, rehabilitative, and sporting settings. However, very little is known regarding the impact of cooling on the microcirculatory response. Objectives: The present study sought to examine the influence of two commonly employed modalities of cryotherapy, whole body cryotherapy (WBC; -110°C) and cold water immersion(CWI; 8±1°C), on skin microcirculation in the mid- thigh region. Methods: The skin area examined was a 3 × 3 cm located between the most anterior aspect of the inguinal fold and the patella. Following 10 minutes of rest, 5 healthy, active males were exposed to either WBC for 3 minutes or CWI for 5 minutes in a randomised order. Volunteers lay supine for five minutes after treatment, in order to monitor the variation of red blood cell (RBC) concentration in the region of interest for a duration of 40 minutes. Microcirculation response was assessed using a non-invasive, portable instrument known as a Tissue Viability imaging system. After a minimum of seven days, the protocol was repeated. Subjective assessment of the volunteer’s thermal comfort and thermal sensation was also recorded. Results: RBC was altered following exposure to both WBC and CWI but appeared to stabilise approximately 35 minutes after treatments. Both WBC and CWI affected thermal sensation (p < 0.05); however no betweengroup differences in thermal comfort or sensation were recorded (p > 0.05). Conclusions: As both WBC and CWI altered RBC, further study is necessary to examine the mechanism for this alteration during whole body cooling.

Numerical simulations of particle deposition in metal foam heat exchangers

Australia is a high-potential country for geothermal power with reserves currently estimated in the tens of millions of petajoules, enough to power the nation for at least 1000 years at current usage. However, these resources are mainly located in isolated arid regions where water is scarce. Therefore, wet cooling systems for geothermal plants in Australia are the least attractive solution and thus air-cooled heat exchangers are preferred. In order to increase the efficiency of such heat exchangers, metal foams have been used. One issue raised by this solution is the fouling caused by dust deposition. In this case, the heat transfer characteristics of the metal foam heat exchanger can dramatically deteriorate. Exploring the particle deposition property in the metal foam exchanger becomes crucial. This paper is a numerical investigation aimed to address this issue. Two dimensional (2D) numerical simulations of a standard one-row tube bundle wrapped with metal foam in cross-flow are performed and highlight preferential particle deposition areas.

Numerical simulations of particle deposition in metal foam heat exchangers

Australia is a high potential country for geothermal power with reserves currently estimated in the tens of millions of petajoules, enough to power the nation for at least 1000 years at current usage.However, these resources are mainly located in isolated arid regions where water is scarce. Therefore, wet cooling systems for geothermal plants in Australia are the least attractive solution and thus air-cooled heat exchangers are preferred. In order to increase the efficiency of such heat exchangers, metal foams have been used. One issue raised by this solution is the fouling caused by dust deposition. In this case, the heat transfer characteristics of the metal foam heat exchanger can dramatically deteriorate. Exploring the particle deposition property in the metal foam exchanger becomes crucial. This paper is a numerical investigation aimed to address this issue. Two-dimensional(2D numerical simulations of a standard one-row tube bundle wrapped with metal foam in cross-flow are performed and highlight preferential particle deposition areas.

Nonlinear pre-fire and post-fire analysis of steel frames

A numerical procedure based on the plastic hinge concept for study of the structural behaviour of steel framed structures exposed to fire is described. Most previous research on fire analysis considered the structural performance due to rising temperature. When strain reversal occurs during the cooling phase, the stress–strain curve is different. The plastic deformation is incorporated into the stress–strain curve to model the strain reversal effect in which unloading under elastic behaviour is allowed. This unloading response is traced by the incremental–iterative Newton–Raphson method. The mechanical properties of the steel member in the present fire analysis follows both Eurocode 3 Part 1.2 and BS5950 Part 8, which implicitly allow for thermal creep deformation. This paper presents an efficient fire analysis procedure for predicting thermal and cooling effects on an isolated element and a multi-storey frame. Several numerical and experimental examples related to structural behaviour in cooling phase are studied and compared with results obtained by other researchers. The proposed method is effective in the fire safety design and analysis of a building in a real fire scenario. The scope of investigation is of great significance since a large number of rescuers would normally enter a fire site as soon as the fire is extinguished and during the cooling phase, so a structural collapse can be catastrophic.

The optimal temperature of first aid treatment for partial thickness burn injuries

Using our porcine model of deep dermal partial thickness burn injury, various cooling techniques (15 degrees C running water, 2 degrees C running water, ice) of first aid were applied for 20 minutes compared with a control (ambient temperature). The subdermal temperatures were monitored during the treatment and wounds observed and photographed weekly for 6 weeks, observing reepithelialization, wound surface area and cosmetic appearance. Tissue histology and scar tensile strength were examined 6 weeks after burn. The 2 degrees C and ice treatments decreased the subdermal temperature the fastest and lowest, however, generally the 15 and 2 degrees C treated wounds had better outcomes in terms of reepithelialization, scar histology, and scar appearance. These findings provide evidence to support the current first aid guidelines of cold tap water (approximately 15 degrees C) for 20 minutes as being beneficial in helping to heal the burn wound. Colder water at 2 degrees C is also beneficial. Ice should not be used.