Stacey Barnes Review of 2012-­‐2 “Epigenomic landscape changes caused by generalist aphid feeding” Score = Good This proposal aims to characterize the epigenetic changes incurred as a result of aphid infestation using the model plant Arabidopsis thaliana and green peach aphids. The proposal has 3 objectives; the first objective is to establish correlations between host DNA methylation and gene expression changes due to aphid infestation. Methylation analysis will be conducted using bisulfite-­‐sequencing technologies made available by Illumina. The gene expression values will be taken from a previously published study by an unrelated lab. The second objective proposes to correlate host gene expression analysis with histone modifications using chromatin immunoprecipitation sequencing analysis (ChIP-­‐seq). This will again use gene expression values from the previously published journal article. The final objective is to create small RNA libraries of infested and uninfested tissue, which will be sequenced using Illumina HiSeq to establish links to changes in host gene expression. The main strengths of this proposal with regards to its scientific merit are; it is a novel idea that feasibly utilizes modern technologies, it will provide information that is relevant to many pathological systems and they have good hypotheses. The proposal would utilize high throughput sequencing technologies to expand on what has currently been observed in a few genes. In each section they have a more specific hypothesis as to what they would like to pay particular attention to after the high throughput sequencing data is collected. This is a big strength as it highlights that they are not just doing high throughput sequencing as a way to collect data and then create hypotheses after their analysis. The main weaknesses of this proposal with regards to its scientific merit are; the utilization of exteriorly performed gene expression analysis and a lack of explanation of the time point being used for tissue harvesting. The current plan is to verify consistency between their study and a previous gene expression study using qRT-­‐PCR of 30 genes. The problem is that this will not be performed until after the sequencing has already occurred so if problems are identified then the dataset maybe wasted. It would be better to perform both analyses on the same tissue to ensure consistency from the outset. The first objective states that tissue will be harvested 72 hours after infestation; it is then assumed that this time point will be used throughout the other objectives. The proposal needs to address why this time point is the most optimal to serve as a representative of epigenetic changes resulting from infestation. The broader impact of this study is evident with respect to its applicability to further work in Arabidopsis thaliana and the possibility for more epigenetic analyses. This section could have been strengthened by offering some insight into how this could be applied to a natural host plant of green peach aphids. Overall this proposal is scored as good because it proposes novel ideas to further a scientific hot topic. It could have been strengthen by proposing to do parallel gene expression analyses as well as elaborating on how this can be applied to economically important crops. Stacey Barnes Review of 2010-­‐1 “Cell-­‐to-­‐cell movment of Potyviruses” Score = Fair This proposal aims to characterize the cell-­‐to-­‐cell movement of Potyvirus using the model Turnip Mosaic Virus (TuMV) and Arabidopsis thaliana. The proposal has two objectives; the first objective is to observe the cell-­‐to-­‐cell movement of the virus using electron microscopy and fluorescent microscopy. This objective is hoping to understand whether the virus moves from cell-­‐to-­‐cell as a virion or as a ribonucleoprotein complex. The second objective aims to elucidate the mechanism by which the virus is able to spread from cell-­‐to-­‐
cell. A yeast two-­‐hybrid screen is proposed to identify host cytoskeleton or secretory pathway proteins that interact with putative viral movement proteins. Interactors identified in the yeast two-­‐hybrid screen will be confirmed using bimolecular fluorescence complementation and co-­‐immunoprecipitation. Also chemicals will be used to disrupt cytoskeleton components to observe how cell-­‐to-­‐cell movement is affected, no details are provided on how this will be observed. The main strength of this proposal with regards to its scientific merit is the attainability of each of the objectives. The methods that this proposal would utilize are frequently published in scientific literature so there is a high probability of success. The idea to use two different methods for visualization of the virus provides even more robustness to the success of the first objective. The main weaknesses of this proposal with regards to its scientific merit are; a lack of novelty or uniqueness, its inability to demonstrate its importance within the field and a lack of justification of the chosen experimental model. It is understood that these techniques can provide knowledge of TuMV at a level similar to that of other viruses. It does, however, lack the ability to build on that knowledge to offer novel insights to the wider virology community. The use of Arabidopsis thaliana for this proposal is not well justified and the proposal fails to offer any insight into the relevancy of the findings and how they will be applied in the virus’s natural host. As stated above, the broader impacts of this proposal are questionable. The main strength would be that the proposal does explain the wide host range of Potyvirus, which emphasizes its economical importance. The main weakness is that the proposal highlights some advantages of using Arabidopsis thaliana but the advantages listed do not clearly coincide with the objectives. One example is that there is a large availability of mutants available for Arabidopsis yet there is no mention of utilizing these mutants in the objectives. Overall this proposal is scored as fair because although it has a high probability of success, it is lacking in an explanation of why this model is the most advantageous. It is lacking in novelty and demonstrates a very narrow focus. Finally the critical evaluation of current literature is poor and fails to explain how many potential proteins will be used in the second objective making it hard to assess the time and economic validity of the proposal.