Climate Change and Greenhouse Gas Awareness Study

This study falls within the enhancing awareness and understanding theme of the National Climate Change Strategy. It was conducted by Agriculture and Agri-Food Canada in January/February 2001 and involved 1,643 farming operation, feeder cattle, dairy cattle, hogs and poultry producers. The purpose of this study is to assess producers' level of awareness of climate change and greenhouse gas (GHG) emissions as well as their understanding of the role of agriculture in the emissions of GHG. This study also establishes a baseline measurement that will be used to evaluate the success of the awareness and public education effort regarding climate change and GHG.climate change, greenhouse gas emissions, emission targets, kyoto protocol, national climate change process, survey, Farm Management, Research Methods/ Statistical Methods,

RNA G-quadruplexes and their potential regulatory roles in translation

Abstract: DNA guanine (G)-rich 4-stranded helical nucleic acid structures called G-quadruplexes (G4), have been extensively studied during the last decades. However, emerging evidence reveals that 50- and 30-untranslated regions (50- and 30-UTRs) as well as open reading frames (ORFs) contain putative RNA G-quadruplexes. These stable secondary structures play key roles in telomere homeostasis and RNA metabolism including pre-mRNA splicing, polyadenylation, mRNA targeting and translation. Interestingly, multiple RNA binding proteins such as nucleolin, FMRP, DHX36, and Aven were identified to bind RNA G-quadruplexes. Moreover, accumulating reports suggest that RNA G-quadruplexes regulate translation in cap-dependent and -independent manner. Herein, we discuss potential roles of RNA G-quadruplexes and associated trans-acting factors in the regulation of mRNA translation

Road User Detection in Videos

Successive frames of a video are highly redundant, and the most popular object detection methods do not take advantage of this fact. Using multiple consecutive frames can improve detection of small objects or difficult examples and can improve speed and detection consistency in a video sequence, for instance by interpolating features between frames. In this work, a novel approach is introduced to perform online video object detection using two consecutive frames of video sequences involving road users. Two new models, RetinaNet-Double and RetinaNet-Flow, are proposed, based respectively on the concatenation of a target frame with a preceding frame, and the concatenation of the optical flow with the target frame. The models are trained and evaluated on three public datasets. Experiments show that using a preceding frame improves performance over single frame detectors, but using explicit optical flow usually does not

Road User Detection in Videos

Successive frames of a video are highly redundant, and the most popular object detection methods do not take advantage of this fact. Using multiple consecutive frames can improve detection of small objects or difficult examples and can improve speed and detection consistency in a video sequence, for instance by interpolating features between frames. In this work, a novel approach is introduced to perform online video object detection using two consecutive frames of video sequences involving road users. Two new models, RetinaNet-Double and RetinaNet-Flow, are proposed, based respectively on the concatenation of a target frame with a preceding frame, and the concatenation of the optical flow with the target frame. The models are trained and evaluated on three public datasets. Experiments show that using a preceding frame improves performance over single frame detectors, but using explicit optical flow usually does not

A conserved target site in HIV-1 Gag RNA is accessible to inhibition by both an HDV ribozyme and a short hairpin RNA

Abstract: Antisense-based molecules targeting HIV-1 RNA have the potential to be used as part of gene or drug therapy to treat HIV-1 infection. In this study, HIV-1 RNA was screened to identify more conserved and accessible target sites for ribozymes based on the hepatitis delta virus motif. Using a quantitative screen for effects on HIV-1 production, we identified a ribozyme targeting a highly conserved site in the Gag coding sequence with improved inhibitory potential compared to our previously described candidates targeting the overlapping Tat/Rev coding sequence. We also demonstrate that this target site is highly accessible to short hairpin directed RNA interference, suggesting that it may be available for the binding of antisense RNAs with different modes of action. We provide evidence that this target site is structurally conserved in diverse viral strains and that it is sufficiently different from the human transcriptome to limit off-target effects from antisense therapies. We also show that the modified hepatitis delta virus ribozyme is more sensitive to a mismatch in its target site compared to the short hairpin RNA. Overall, our results validate the potential of a new target site in HIV-1 RNA to be used for the development of antisense therapies

Unbiased in vitro selection reveals the unique character of the self-cleaving antigenomic HDV RNA sequence

In order to revisit the architecture of the catalytic center of the antigenomic hepatitis delta virus (HDV) ribozyme we developed an unbiased in vitro selection procedure that efficiently selected novel variants from a relatively small set of sequences. Using this procedure we examined all possible variants from a pool of HDV ribozymes that had been randomized at 25 positions (4(25)). The isolated set of sequences shows more variability than do the natural variants. Nucleotide variations were found at all randomized positions, even at positions when the general belief was that the specific base was absolutely required for catalytic activity. Covariation analysis supports the presence of several base pairs, although it failed to propose any new tertiary contacts. HDV ribozyme appears to possess a greater number of constraints, in terms of sequences capable of supporting the catalysed cleavage, than do other catalytic RNAs. This supports the idea that the appearance of this catalytic RNA structure has a low probability (i.e. is a rare event), which may explain why to date it has been found in nature only in the HDV. These contrasts with the hammerhead self-cleaving motif that is proposed to have multiple origins, and that is widespread among different organisms. Thus, just because a self-cleaving RNA motif is small does not imply that it occurs easily

Exploring mRNA 3'-UTR G-quadruplexes: evidence of roles in both alternative polyadenylation and mRNA shortening

Abstract: Guanine-rich RNA sequences can fold into noncanonical, four stranded helical structures called G-quadruplexes that have been shown to be widely distributed within the mammalian transcriptome, as well as being key regulatory elements in various biological mechanisms. That said, their role within the 30-untranslated region (UTR) of mRNA remains to be elucidated and appreciated. A bioinformatic analysis of the 30-UTRs of mRNAs revealed enrichment in G-quadruplexes. To shed light on the role(s) of these structures, those found in the LRP5 and FXR1 genes were characterized both in vitro and in cellulo. The 30- UTR G-quadruplexes were found to increase the efficiencies of alternative polyadenylation sites, leading to the expression of shorter transcripts and to possess the ability to interfere with the miRNA regulatory network of a specific mRNA. Clearly, G-quadruplexes located in the 30-UTRs of mRNAs are cis-regulatory elements that have a significant impact on gene expression

Target-dependent on/off switch increases ribozyme fidelity

Ribozymes, RNA molecules that catalyze the cleavage of RNA substrates, provide an interesting alternative to the RNA interference (RNAi) approach to gene inactivation, especially given the fact that RNAi seems to trigger an immunological response. Unfortunately, the limited substrate specificity of ribozymes is considered to be a significant hurdle in their development as molecular tools. Here, we report the molecular engineering of a ribozyme possessing a new biosensor module that switches the cleavage activity from ‘off’ (a ‘safety lock’) to ‘on’ solely in the presence of the appropriate RNA target substrate. Both proof-of-concept and the mechanism of action of this man-made riboswitch are demonstrated using hepatitis delta virus ribozymes that cleave RNA transcripts derived from the hepatitis B and C viruses. To our knowledge, this is the first report of a ribozyme bearing a target-dependent module that is activated by its RNA substrate, an arrangement which greatly diminishes non-specific effects. This new approach provides a highly specific and improved tool with significant potential for application in the fields of both functional genomics and gene therapy

The super-n-motifs model : a novel alignment-free approach for representing and comparing RNA secondary structures

Abstract : Motivation: Comparing ribonucleic acid (RNA) secondary structures of arbitrary size uncovers structural patterns that can provide a better understanding of RNA functions. However, performing fast and accurate secondary structure comparisons is challenging when we take into account the RNA configuration (i.e. linear or circular), the presence of pseudoknot and G-quadruplex (G4) motifs and the increasing number of secondary structures generated by high-throughput probing techniques. To address this challenge, we propose the super-n-motifs model based on a latent analysis of enhanced motifs comprising not only basic motifs but also adjacency relations. The super-n-motifs model computes a vector representation of secondary structures as linear combinations of these motifs. Results: We demonstrate the accuracy of our model for comparison of secondary structures from linear and circular RNA while also considering pseudoknot and G4 motifs. We show that the supern- motifs representation effectively captures the most important structural features of secondary structures, as compared to other representations such as ordered tree, arc-annotated and string representations. Finally, we demonstrate the time efficiency of our model, which is alignment free and capable of performing large-scale comparisons of 10 000 secondary structures with an efficiency up to 4 orders of magnitude faster than existing approaches