Reduction in weed seedling emergence by pathogens following the incorporation of green crop residue

Summary Because tillage promotes the germination of many weed species and freshly killed plant material favours the growth of microbial pathogens, we hypothesised that the incorporation of green crop residue should temporarily reduce weed seedling emergence relative to unamended soil. Soil with field-incorporated green crop residue was compared with non-amended soil in glasshouse experiments by sowing several weed species at different times after incorporation. Species included Abutilon theophrasti, Chenopodium album, Amaranthus powellii, Setaria faberi, Echinochloa crus-galli and, in one year, lettuce and red clover. Soils with green crop residue reduced seedling emergence for 0-4 days after incorporation by an average of 30%. Comparison of emergence in nonsterilised soil with that in sterilised soil, with and without fresh crop residue, indicated that a biological agent caused the depressed emergence. In the third year of the study, the fungi Fusarium oxysporum and F. chlamydosporum were isolated from seeds exposed to soil amended with green crop residues, and their pathogenicity to seeds and seedlings was confirmed in bioassays. This study indicated that incorporation of fresh crop residue reduces the first flush of weed seedlings following tillage and that this depression in emergence is probably caused by pathogen attack on seeds and seedlings before emergence

Revealing the density of encoded functions in a viral RNA

Nikesh Patel, et al, ‘Revealing the density of encoded functions in a viral RNA’, Proceedings of the National Academy of Sciences of the United States of America (PNAS), Vol. 112 (7): 2227-2232, February 2015, doi: http:dx.doi.org/10. 1073/pnas.1420812112. This article is freely available online through the PNAS open access option.We present direct experimental evidence that assembly of a single-stranded RNA virus occurs via a packaging signal-mediated mechanism. We show that the sequences of coat protein recognition motifs within multiple, dispersed, putative RNA packaging signals, as well as their relative spacing within a genomic fragment, act collectively to influence the fidelity and yield of capsid self-assembly in vitro. These experiments confirm that the selective advantages for viral yield and encapsidation specificity, predicted from previous modeling of packaging signal-mediated assembly, are found in Nature. Regions of the genome that act as packaging signals also function in translational and transcriptional enhancement, as well as directly coding for the coat protein, highlighting the density of encoded functions within the viral RNA. Assembly and gene expression are therefore direct molecular competitors for different functional folds of the same RNA sequence. The strongest packaging signal in the test fragment, encodes a region of the coat protein that undergoes a conformational change upon contact with packaging signals. A similar phenomenon occurs in other RNA viruses for which packaging signals are known. These contacts hint at an even deeper density of encoded functions in viral RNA, which if confirmed, would have profound consequences for the evolution of this class of pathogensPeer reviewedFinal Published versio

Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging

The specific packaging of the hepatitis C virus (HCV) genome is hypothesised to be driven by Core- RNA interactions. To identify the regions of the viral genome involved in this process, we used SELEX (systematic evolution of ligands by exponential enrichment) to identify RNA aptamers which bind specifically to Core in vitro. Comparison of these aptamers to multiple HCV genomes revealed the presence of a conserved terminal loop motif within short RNA stem-loop structures. We postulated that interactions of these motifs, as well as sub-motifs which were present in HCV genomes at statistically significant levels, with the Core protein may drive virion assembly. We mutated 8 of these predicted motifs within the HCV infectious molecular clone JFH-1, thereby producing a range of mutant viruses predicted to possess altered RNA secondary structures. RNA replication and viral titre were unaltered in viruses possessing only one mutated structure. However, infectivity titres were decreased in viruses possessing a higher number of mutated regions. This work thus identified multiple novel RNA motifs which appear to contribute to genome packaging. We suggest that these structures act as cooperative packaging signals to drive specific RNA encapsidation during HCV assembly

Integration of FIRST, FRODA and NMM in a coarse grained method to study Protein Disulphide Isomerase conformational change

Our simulations of protein motion are based on a rigidity-based coarse graining criteria which is able to identify flexible and constraint regions and on Normal Modes of Motion (NMM) which map out the directions of motion for a given network. The NMM and rigidity constraints are integrated together by the FRODA module to identify large scale conformational changes at low computational cost. In this context we identify the limits for conformational change of a large multi domain protein -Protein Disulphide Isomerase, by re-assessing the principal NMM at intermediate points along a trajectory as the protein moves over the trajectory defined by the initial principal NMM

Parameterizing Elastic Network Models to Capture the Dynamics of Proteins

International audienceCoarse-grained normal mode analyses of protein dynamics rely on the idea that the geometry of a protein structure contains enough information for computing its fluctuations around its equilibrium conformation. This geometry is captured in the form of an elastic network (EN), namely a network of edges between its residues. The normal modes of a protein are then identified with the normal modes of its EN. Different approaches have been proposed to construct ENs, focusing on the choice of the edges that they are comprised of, and on their parameterizations by the force constants associated with those edges. Here we propose new tools to guide choices on these two facets of EN. We study first different geometric models for ENs. We compare cutoff-based ENs, whose edges have lengths that are smaller than a cutoff distance, with Delaunay-based ENs and find that the latter provide better representations of the geometry of protein structures. We then derive an analytical method for the parameterization of the EN such that its dynamics leads to atomic fluctuations that agree with experimental Bfactors. To limit overfitting, we attach a parameter referred to as flexibility constant to each atom instead of to each edge in the EN. The parameterization is expressed as a non-linear optimization problem whose parameters describe both rigid-body and internal motions. We show that this parameterization leads to improved ENs, whose dynamics mimic MD simulations better than ENs with uniform force constants, and reduces the number of normal modes needed to reproduce functional conformational changes

Planning and implementation of a participatory evaluation strategy: A viable approach in the evaluation of community-based participatory programs addressing cancer disparities

Community-based participatory research (CBPR) has been posited as a promising methodology to address health concerns at the community level, including cancer disparities. However, the major criticism to this approach is the lack of scientific grounded evaluation methods to assess development and implementation of this type of research. This paper describes the process of development and implementation of a participatory evaluation framework within a CBPR program to reduce breast, cervical, and colorectal cancer disparities between African Americans and whites in Alabama and Mississippi as well as lessons learned. The participatory process involved community partners and academicians in a fluid process to identify common ground activities and outcomes. The logic model, a lay friendly approach, was used as the template and clearly outlined the steps to be taken in the evaluation process without sacrificing the rigorousness of the evaluation process. We have learned three major lessons in this process: (1) the importance of constant and open dialogue among partners; (2) flexibility to make changes in the evaluation plan and implementation; and (3) importance of evaluators playing the role of facilitators between the community and academicians. Despite the challenges, we offer a viable approach to evaluation of CBPR programs focusing on cancer disparitie