Advanced Engineering of Lipid Metabolism in Nicotiana benthamiana Using a Draft Genome and the V2 Viral Silencing-Suppressor Protein

The transient leaf assay in Nicotiana benthamiana is widely used in plant sciences, with one application being the rapid assembly of complex multigene pathways that produce new fatty acid profiles. This rapid and facile assay would be further improved if it were possible to simultaneously overexpress transgenes while accurately silencing endogenes. Here, we report a draft genome resource for N. benthamiana spanning over 75% of the 3.1 Gb haploid genome. This resource revealed a two-member NbFAD2 family, NbFAD2.1 and NbFAD2.2, and quantitative RT-PCR (qRT-PCR) confirmed their expression in leaves. FAD2 activities were silenced using hairpin RNAi as monitored by qRT-PCR and biochemical assays. Silencing of endogenous FAD2 activities was combined with overexpression of transgenes via the use of the alternative viral silencing-suppressor protein, V2, from Tomato yellow leaf curl virus. We show that V2 permits maximal overexpression of transgenes but, crucially, also allows hairpin RNAi to operate unimpeded. To illustrate the efficacy of the V2-based leaf assay system, endogenous lipids were shunted from the desaturation of 18:1 to elongation reactions beginning with 18:1 as substrate. These V2-based leaf assays produced ~50% more elongated fatty acid products than p19-based assays. Analyses of small RNA populations generated from hairpin RNAi against NbFAD2 confirm that the siRNA population is dominated by 21 and 22 nt species derived from the hairpin. Collectively, these new tools expand the range of uses and possibilities for metabolic engineering in transient leaf assays. © 2012 Naim et al.

De Novo Transcriptome Sequence Assembly and Analysis of RNA Silencing Genes of Nicotiana benthamiana

Background: Nicotiana benthamiana has been widely used for transient gene expression assays and as a model plant in the study of plant-microbe interactions, lipid engineering and RNA silencing pathways. Assembling the sequence of its transcriptome provides information that, in conjunction with the genome sequence, will facilitate gaining insight into the plant's capacity for high-level transient transgene expression, generation of mobile gene silencing signals, and hyper-susceptibility to viral infection. Methodology/Results: RNA-seq libraries from 9 different tissues were deep sequenced and assembled, de novo, into a representation of the transcriptome. The assembly, of16GB of sequence, yielded 237,340 contigs, clustering into 119,014 transcripts (unigenes). Between 80 and 85% of reads from all tissues could be mapped back to the full transcriptome. Approximately 63% of the unigenes exhibited a match to the Solgenomics tomato predicted proteins database. Approximately 94% of the Solgenomics N. benthamiana unigene set (16,024 sequences) matched our unigene set (119,014 sequences). Using homology searches we identified 31 homologues that are involved in RNAi-associated pathways in Arabidopsis thaliana, and show that they possess the domains characteristic of these proteins. Of these genes, the RNA dependent RNA polymerase gene, Rdr1, is transcribed but has a 72 nt insertion in exon1 that would cause premature termination of translation. Dicer-like 3 (DCL3) appears to lack both the DEAD helicase motif and second dsRNA binding motif, and DCL2 and AGO4b have unexpectedly high levels of transcription. Conclusions: The assembled and annotated representation of the transcriptome and list of RNAi-associated sequences are accessible at www.benthgenome.com alongside a draft genome assembly. These genomic resources will be very useful for further study of the developmental, metabolic and defense pathways of N. benthamiana and in understanding the mechanisms behind the features which have made it such a well-used model plant. © 2013 Nakasugi et al.

The use of artificial MicroRNA technology to control gene expression in Arabidopsis thaliana

In plants, double-stranded RNA (dsRNA) is an effective trigger of RNA silencing, and several classes of endogenous small RNA (sRNA), processed from dsRNA substrates by DICER-like (DCL) endonucleases, are essential in controlling gene expression. One such sRNA class, the microRNAs (miRNAs) control the expression of closely related genes to regulate all aspects of plant development, including the determination of leaf shape, leaf polarity, flowering time, and floral identity. A single miRNA sRNA silencing signal is processed from a long precursor transcript of nonprotein-coding RNA, termed the primary miRNA (pri-miRNA). A region of the pri-miRNA is partially self-complementary allowing the transcript to fold back onto itself to form a stem-loop structure of imperfectly dsRNA. Artificial miRNA (amiRNA) technology uses endogenous pri-miRNAs, in which the miRNA and miRNA*(passenger strand of the miRNA duplex) sequences have been replaced with corresponding amiRNA/ amiRNA*sequences that direct highly efficient RNA silencing of the targeted gene. Here, we describe the rules for amiRNA design, as well as outline the PCR and bacterial cloning procedures involved in the construction of an amiRNA plant expression vector to control target gene expression in Arabidopsis thaliana. © 2014 Springer Science+Business Media New York.

A suite of novel promoters and terminators for plant biotechnology II. The pPLEX series for use in monocots

A suite of plant expression vectors (pPLEX), constructed from the gene regulation signals from subterranean clover stunt virus (SCSV) genome, has previously been used in dicot transformation for a variety of applications in plant biotechnology. To assess their use for the transformation of monocots, a number of modifications were made to the basic vector series and assessed in rice. In their unmodified forms, the SCSV promoters directed low levels of gene expression, however, insertion of an intron between the promoter and the transgene open reading frame (analogous to the rice actin and maize ubiquitin promoter systems) increased transgene expression 50-fold. The expression patterns from the intron-modified SCSV (segments 4 and 7) promoters were very similar to those directed by the actin or ubiquitin promoters. All promoter systems investigated directed expression that appeared to be constitutive within leaf tissue, and localised to the epidermal and vascular tissues of the root. The pPLEX vectors described here are an important counterpart to the dicot pPLEX series and have the potential to be useful in monocot research and biotechnology.

Assessing land-use and transport integration via a spatial composite indexing model

Achieving sustainable urban development is identified as one ultimate goal of many contemporary planning endeavours and has become central to formulation of urban planning policies. Within this concept, land-use and transport integration is highlighted as one of the most important and attainable policy objectives. In many cities, integration is embraced as an integral part of local development plans, and a number of key integration principles are identified. However, the lack of available evaluation methods to measure extent of urban sustainability levels prevents successful implementation of these principles. This paper introduces a new indicator-based spatial composite indexing model developed to measure sustainability performance of urban settings by taking into account land-use and transport integration principles. Model indicators are chosen via a thorough selection process in line with key principles of land-use and transport integration. These indicators are grouped into categories and themes according to their topical relevance. These indicators are then aggregated to form a spatial composite index to portray an overview of the sustainability performance of the pilot study area used for model demonstration. The study results revealed that the model is a practical instrument for evaluating success of local integration policies and visualizing sustainability performance of built environments and useful in both identifying problematic areas as well as formulating policy interventions.

Comparison of promoters and selectable marker genes for use in Indica rice transformation

The effectiveness of different promoters for use in Indica rice transformation was compared. Plasmids encoding the Escherichia coli uidA (gus) gene under the control of CaMV 35S, Emu, Act1 or Ubi1 promoters were delivered into cell suspension cultures by particle bombardment. Transient gene expression, 48 h after delivery, was greatest from plasmids utilising the constitutive promoters, Act1 and Ubi1. Gene expression in stably transformed tissue was examined by bombarding embryogenic Indica rice calli with a pUbil-gus plasmid and a plasmid containing either the selectable marker gene, hph, which confers hygromycin resistance, or bar, which confers resistance to the herbicide phosphinothricin (BASTA) each under the control of the CaMV 35S, Emu, Act1 or the Ubi1 promoters. The bombarded calli were placed on the appropriate selection media and stained for GUS activity at 1 day, 3 weeks and 5 weeks after shooting. Callus bombarded with the pUbi1-hph or the pEmu-hph constructs gave a dramatic increase in the size of the GUS staining areas with time. No such increase in the size of GUS staining areas was observed in calli co-bombarded with pUbi1-gus and any of the bar containing constructs. Co-bombardment of calli with either the pEmu-hph or pUbi1-hph construct and a virus minor coat protein (cp) gene construct resulted in many fertile transgenic Indica rice plants, containing one to eight copies of both the hph and cp genes. These genes were stably inherited by the T 1 generation.

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.

Australian Research to Encourage School Students’ Positive Use of Technology to Reduce Cyberbullying

Information and Communications Technology (ICT) has spread rapidly in Australia. Mobile phones, which increasingly have advanced capabilities including Internet access, mobile television and multimedia storage, are owned by 22% of Australian children aged 9-11 years and 73% of those aged 12-14 years (Australian Bureau of Statistics, 2012b), as well as by over 90% of Australians aged 15 years and over(Australian Communications and Media Authority (ACMA), 2010). Nearly 80% of Australian households have access to the Internet and 73% have a broadband Internet connection, ensuring that Internet access is typically reliable and high-speed (Australian Bureau of Statistics, 2012a). Ninety percent of Australian children aged 5-14 years (comprising 79% of 5-8 year olds; 96% of 9-11 year olds; and 98% of 12-14 year olds) reported having accessed the Internet during 2011-2012, a significant increase from 79% in 2008-2009 (Australian Bureau of Statistics, 2012b). Approximately 90% of 5-14 year olds have accessed the Internet both from home and from school, with close to 49% accessing the Internet from other places (Australian Bureau of Statistics, 2012b). Young people often make use of borrowed Internet access (e.g. in friends’ homes), commercial access (e.g. cybercafés), public access (e.g. libraries), and mobile device access in areas offering free Wi-Fi (Lim, 2009).

Pitfalls in the use of kappa when interpreting agreement between multiple raters in reliability studies

OBJECTIVE To compare different reliability coefficients (exact agreement, and variations of the kappa (generalised, Cohen's and Prevalence Adjusted and Biased Adjusted (PABAK))) for four physiotherapists conducting visual assessments of scapulae. DESIGN Inter-therapist reliability study. SETTING Research laboratory. PARTICIPANTS 30 individuals with no history of neck or shoulder pain were recruited with no obvious significant postural abnormalities. MAIN OUTCOME MEASURES Ratings of scapular posture were recorded in multiple biomechanical planes under four test conditions (at rest, and while under three isometric conditions) by four physiotherapists. RESULTS The magnitude of discrepancy between the two therapist pairs was 0.04 to 0.76 for Cohen's kappa, and 0.00 to 0.86 for PABAK. In comparison, the generalised kappa provided a score between the two paired kappa coefficients. The difference between mean generalised kappa coefficients and mean Cohen's kappa (0.02) and between mean generalised kappa and PABAK (0.02) were negligible, but the magnitude of difference between the generalised kappa and paired kappa within each plane and condition was substantial; 0.02 to 0.57 for Cohen's kappa and 0.02 to 0.63 for PABAK, respectively. CONCLUSIONS Calculating coefficients for therapist pairs alone may result in inconsistent findings. In contrast, the generalised kappa provided a coefficient close to the mean of the paired kappa coefficients. These findings support an assertion that generalised kappa may lead to a better representation of reliability between three or more raters and that reliability studies only calculating agreement between two raters should be interpreted with caution. However, generalised kappa may mask more extreme cases of agreement (or disagreement) that paired comparisons may reveal.

Modeling predictors of risky drug use behavior among male street laborers in urban Vietnam

Background The application of theoretical frameworks for modeling predictors of drug risk among male street laborers remains limited. The objective of this study was to test a modified version of the IMB (Information-Motivation-Behavioral Skills Model), which includes psychosocial stress, and compare this modified version with the original IMB model in terms of goodness-of-fit to predict risky drug use behavior among this population. Methods In a cross-sectional study, social mapping technique was conducted to recruit 450 male street laborers from 135 street venues across 13 districts of Hanoi city, Vietnam, for face-to-face interviews. Structural equation modeling (SEM) was used to analyze data from interviews. Results Overall measures of fit via SEM indicated that the original IMB model provided a better fit to the data than the modified version. Although the former model was able to predict a lesser variance than the latter (55% vs. 62%), it was of better fit. The findings suggest that men who are better informed and motivated for HIV prevention are more likely to report higher behavioral skills, which, in turn, are less likely to be engaged in risky drug use behavior. Conclusions This was the first application of the modified IMB model for drug use in men who were unskilled, unregistered laborers in urban settings. An AIDS prevention program for these men should not only distribute information and enhance motivations for HIV prevention, but consider interventions that could improve self-efficacy for preventing HIV infection. Future public health research and action may also consider broader factors such as structural social capital and social policy to alter the conditions that drive risky drug use among these men.

Use and usefulnss of PDSs in the financial planning context

Following considerable criticism of the complexity and lack of readability of product disclosure statements (PDSs), regulatory changes were introduced requiring shorter PDSs for certain investment products. This paper reports the findings of an online survey of financial planners regarding use of managed investment scheme (MIS) PDSs with clients, the perceived usefulness of PDSs as an information source, and their views on shorter PDSs. Our findings highlight major concerns about the usefulness of the PDS and disclosure reforms.

Possible, inevitable or fait accompli? An analysis of streaming video acquisition, acceptance and use in higher education

This paper explores the potential for online video as a mechanism to transform the ways students learn, as measured by research, user experience and usage following surveys and trials of patron-driven acquisition collaboratively undertaken by Queensland University of Technology, La Trobe University and Kanopy.

Governing young people’s drug use: Crime, harm and contemporary drug use practices

Since the nineteenth century, drug use has been variously understood as a problem of epidemiology, psychiatry, physiology, and criminality. Consequently drug research tends to be underpinned by assumptions of inevitable harm, and is often directed towards preventing drug use or solving problems. These constructions of the drug problem have generated a range of law enforcement responses, drug treatment technologies and rehabilitative programs that are intended to prevent drug related harm and resituate drug users in the realm of neo-liberal functional citizenship. This paper is based on empirical research of young people’s illicit drug use in Brisbane. The research rejects the idea of a pre-given drug problem, and seeks to understand how drugs have come to be defined as a problem. Using Michel Foucault’s conceptual framework of governmentality, the paper explores how the governance of illicit drugs, through law, public health and medicine, intersects with self-governance to shape young people’s drug use practices. It is argued that constructions of the drug problem shape what drug users believe about themselves and the ways in which they use drugs. From this perspective, drug use practices are ‘practices of the self’, formed through an interaction of the government of illicit drugs and the drug users own subjectivity.

Literature review : use of respite by carers of people with dementia

Respite care is a cornerstone service for the home management of people with dementia. It is used by carers to mitigate the stress related to the demands of caring by allowing time for them to rest and do things for themselves, thus maintaining the caring relationship at home and perhaps forestalling long-term placement in a residential aged care facility. Despite numerous anecdotal reports in support of respite care, its uptake by carers of people with dementia remains relatively low. The aim of this paper was to examine the factors that constitute the use of respite by carers of people with dementia by reviewing quantitative and qualitative research predominantly from the years 1990 to 2012. Seventysix international studies of different types of respite care were included for this review and their methods were critically appraised. The key topics identified were in relation to information access, the barriers to carers realising need for and seeking respite, satisfaction with respite services including the outcomes for carers and people with dementia, the characteristics of an effective respite service and the role of health workers in providing appropriate respite care. Finally, limitations with considering the literature as a whole were highlighted and recommendations made for future research.