Effect of 5′UTR introns on gene expression in Arabidopsis thaliana

Background The majority of introns in gene transcripts are found within the coding sequences (CDSs). A small but significant fraction of introns are also found to reside within the untranslated regions (5′UTRs and 3′UTRs) of expressed sequences. Alignment of the whole genome and expressed sequence tags (ESTs) of the model plant Arabidopsis thaliana has identified introns residing in both coding and non-coding regions of the genome. Results A bioinformatic analysis revealed some interesting observations: (1) the density of introns in 5′UTRs is similar to that in CDSs but much higher than that in 3′UTRs; (2) the 5′UTR introns are preferentially located close to the initiating ATG codon; (3) introns in the 5′UTRs are, on average, longer than introns in the CDSs and 3′UTRs; and (4) 5′UTR introns have a different nucleotide composition to that of CDs and 3′UTR introns. Furthermore, we show that the 5′UTR intron of the A. thaliana EFIα-A3 gene affects the gene expression and the size of the 5′UTR intron influences the level of gene expression. Conclusion Introns within the 5′UTR show specific features that distinguish them from introns that reside within the coding sequence and the 3′UTR. In the EFIα-A3 gene, the presence of a long intron in the 5′UTR is sufficient to enhance gene expression in plants in a size dependent manner.

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.

Non-formal techniques for requirements elicitation, modeling, and early assessment for services

Designing systems for multiple stakeholders requires frequent collaboration with multiple stakeholders from the start. In many cases at least some stakeholders lack a professional habit of formal modeling. We report observations from two case studies of stakeholder-involvement in early design where non-formal techniques supported strong collaboration resulting in deep understanding of requirements and of the feasibility of solutions.

Similarity solutions for flow and heat transfer of non-Newtonian fluid over a stretching surface

Similarity solutions are carried out for flow of power law non-Newtonian fluid film on unsteady stretching surface subjected to constant heat flux. Free convection heat transfer induces thermal boundary layer within a semi-infinite layer of Boussinesq fluid. The nonlinear coupled partial differential equations (PDE) governing the flow and the boundary conditions are converted to a system of ordinary differential equations (ODE) using two-parameter groups. This technique reduces the number of independent variables by two, and finally the obtained ordinary differential equations are solved numerically for the temperature and velocity using the shooting method. The thermal and velocity boundary layers are studied by the means of Prandtl number and non-Newtonian power index plotted in curves.

A visual profile of Queensland indigenous and non-indigenous school children, and the association between vision and reading

This research investigated the prevalence of vision disorders in Queensland Indigenous primary school children, creating the first comprehensive visual profile of Indigenous children. Findings showed reduced convergence ability and reduced visual information processing skills were more common in Indigenous compared to non-Indigenous children. Reduced visual information processing skills were also associated with reduced reading outcomes in both groups of children. As early detection of visual disorders is important, the research also reviewed the delivery of screening programs across Queensland and proposed a model for improved coordination and service delivery of vision screening to Queensland school children.

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.

CTCombine : rotating and combining CT data with an accurate detector model to simulate radiotherapy portal imaging at non-zero beam angles

Established Monte Carlo user codes BEAMnrc and DOSXYZnrc permit the accurate and straightforward simulation of radiotherapy experiments and treatments delivered from multiple beam angles. However, when an electronic portal imaging detector (EPID) is included in these simulations, treatment delivery from non-zero beam angles becomes problematic. This study introduces CTCombine, a purpose-built code for rotating selected CT data volumes, converting CT numbers to mass densities, combining the results with model EPIDs and writing output in a form which can easily be read and used by the dose calculation code DOSXYZnrc...

Physical activity and determinants of physical activity in obese and non-obese children

OBJECTIVE To compare the physical activity (PA) patterns and the hypothesized psychosocial and environmental determinants of PA in an ethnically diverse sample of obese and non-obese middle school children. DESIGN Cross-sectional study. SUBJECTS One-hundred and thirty-three non-obese and 54 obese sixth grade children (mean age of 11.4 +/-0.6). Obesity status determined using the age-, race- and gender-specific 95th percentile for BMI from NHANES-1. MEASUREMENTS Objective measurements were collected of PA over a 7-day period using the CSA 7164 accelerometer: total daily counts; daily moderate (3-5.9 METs) physical activity (MPA); daily vigorous physical activity (greater than or equal to 6 METs; VPA); and weekly number of 5, 10 and 20 min bouts of moderate-to-vigorous physical activity (greater than or equal to 3 METs, MVPA). Self-report measures were collected of PA self-efficacy; social influences regarding PA, beliefs about PA outcomes; perceived PA levels of parents and peers, access to sporting and/or fitness equipment at home, involvement in community-based PA organizations; participation in community sports teams; and hours spent watching television or playing video games. RESULTS Compared to their non-obese counterparts, obese children exhibited significantly lower daily accumulations of total counts, MPA and VPA as well as significantly fewer 5, 10 and 20 min bouts of MVPA. Obese children reported significantly lower levels of PA self-efficacy, were involved in significantly fewer community organizations promoting PA and were significantly less likely to report their father or male guardian as physically active. CONCLUSIONS The results are consistent with the hypothesis that physical inactivity is an important contributing factor in the maintenance of childhood obesity. Interventions to promote PA in obese children should endeavor to boost self-efficacy perceptions regarding exercise, increase awareness of, and access to, community PA outlets, and increase parental modeling of PA.

Object tracking via non-Euclidean geometry : a Grassmann approach

A robust visual tracking system requires an object appearance model that is able to handle occlusion, pose, and illumination variations in the video stream. This can be difficult to accomplish when the model is trained using only a single image. In this paper, we first propose a tracking approach based on affine subspaces (constructed from several images) which are able to accommodate the abovementioned variations. We use affine subspaces not only to represent the object, but also the candidate areas that the object may occupy. We furthermore propose a novel approach to measure affine subspace-to-subspace distance via the use of non-Euclidean geometry of Grassmann manifolds. The tracking problem is then considered as an inference task in a Markov Chain Monte Carlo framework via particle filtering. Quantitative evaluation on challenging video sequences indicates that the proposed approach obtains considerably better performance than several recent state-of-the-art methods such as Tracking-Learning-Detection and MILtrack.

Competitive charge-remote and anion-induced fragmentations of the non-8-enoate anion. A charge-remote reaction which co-occurs with hydrogen scrambling

The non-8-enoate anion undergoes losses of the elements of C3H6, C4H8 and C6H12 on collisional activation, The mechanisms of these processes have been elucidated by a combination of product ion and labelling (H-2 and C-13) studies, together with a neutralisation reionisation mass spectrometric study. These studies allow the following conclusions to be made. (i) The loss of C3H6 involves cyclisation of the enolate anion of non-8-enoic acid to yield the cyclopentyl carboxylate anion and propene. (ii) The loss of 'C4H8' is a charge-remote process (one which proceeds remote from the charged centre) which yields the pent-4-enoate anion, butadiene and dihydrogen. This process co-occurs and competes with complex H scrambling. (iii) The major loss of 'C6H12' occurs primarily by a charge-remote process yielding the acrylate anion, hexa-1,5-diene and dihydrogen, but in this case no H scrambling accompanies the process. (iv) It is argued that the major reason why the two charge-remote processes occur in preference to anion-induced losses of but-l-ene and hex-l-ene from the respective 4- and 2-anions is that although these anions are formed, they have alternative and lower energy fragmentation pathways than those involving the losses of but-l-ene and hex-l-ene; viz. the transient 4-anion undergoes facile proton transfer to yield a more stable anion, whereas the 2-(enolate) anion undergoes preferential cyclisation followed by elimination of propene [see (i) above].

The impact of organisational citizenship behaviour and non-material rewards on dimensions of employee burnout : evidence from the teaching profession

In this chapter, we examine the psychological impact that organisational citizenship behaviours (OCBs) have on individuals performing them. OCB is discretionary employee behaviour that is not systematically rewarded by employers, but that contributes to overall organisational effectiveness (Organ, 1988). In a sample of schoolteachers, we predicted that performing OCBs would differentially impact two dimensions of psychological burnout -personal accomplishment (PA} and emotional exhaustion (EE). Due to the volitional nature of OCB, there are theoretical reasons to suppose that OCB enhances PA. However, it is also possible that certain OCBs constitute increased workload, thereby contributing to a heightened sense of EE. In addition, given prior research showing that non-material rewards such as praise and recognition, lead to positive employee outcomes, we proposed that praise and recognition would strengthen the relationship between OCB and PA, and weaken the relationship between OCB and EE.

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...

Validation of a 24-h physical activity recall in indigenous and non-indigenous Australian adolescents

The purpose of this study was to evaluate the concurrent validity of a modified version of the widely used previous day physical activity recall (PDPAR24) self-report instrument in a diverse sample of Australian adolescents comprising Aboriginal and Torres Strait Islanders (A&TSI) and non-indigenous high school students. A sample of 63 A&TSI and 59 non-indigenous high school students (N = 122) from five public secondary schools participated in the study. Participants completed the PDPAR-24 after wearing a seated electronic pedometer on the previous day. Significant positive correlations were observed between the self-reported physical activity variables (mean MET level, blocks of vigorous activity, and blocks of moderate-to-vigorous physical activity) and 24-h step counts. Validity coefficients (rho) ranged from 0.29 to 0.34 (p<0.05). A significant inverse correlation was observed for self-reported screen time and 24-h step count (rho = -0.19, p<0.05). Correlations for A&TSI students were equal to or greater than those observed for non-indigenous students. The PDPAR-24 instrument is a quick, unobtrusive, and cost-effective assessment tool. that would be useful for evaluating physical activity and sedentary behaviour in population-based studies. (C) 2006 Sports Medicine Australia.

MMP-9 secretion and MMP-2 activation distinguish invasive and metastatic sublines of a mouse mammary carcinoma system showing epithelial-mesenchymal transition traits

We have investigated the gelatinase profiles and invasiveness of clonal tumour sublines derived from a spontaneously arising mammary tumour in a Balb/cfC3H mouse. The 67NR, 66c14 and 4T1.2 sublines have low, intermediate and high metastatic potential respectively. In Boyden chamber studies, Matrigel invasion was seen to be progressively higher in the more metastatic lines 4T1.2>66c14>67NR, consistent with MMP-2 activation potential, MMP-9 secretion, and migration over either type I or IV collagen, which were low in both 67NR and 66c14 cells compared to 4T1.2 cells. These attributes are consistent with those seen in human breast cancer cell lines which appear to have undergone an epithelial-mesenchymal transition (EMT) as indicated by vimentin expression. We were, however, surprised to find vimentin expression, MT1-MMP expression and stellate Matrigel outgrowth in the non-invasive, non-metastatic 67NR cells, indicating that they had undergone an EMT despite not being invasive. We conclude that the EMT is manifested to differing degrees in these three clonal cell lines, and that the 67NR cells have either undergone a partial EMT or have since lost certain important attributes of the EMT-derived phenotype. This model should prove useful in further characterizing the regulation of MT1-MMP mediated MMP-2 activation and delineating the EMT in breast cancer progression.

Multiple map hypotheses for planning and navigating in non-stationary environments

This paper presents a method to enable a mobile robot working in non-stationary environments to plan its path and localize within multiple map hypotheses simultaneously. The maps are generated using a long-term and short-term memory mechanism that ensures only persistent configurations in the environment are selected to create the maps. In order to evaluate the proposed method, experimentation is conducted in an office environment. Compared to navigation systems that use only one map, our system produces superior path planning and navigation in a non-stationary environment where paths can be blocked periodically, a common scenario which poses significant challenges for typical planners.