Pollom and Skates: Module 3 Research Proposal Page

'''Background:
''' 1. The recent work in the Belcher Lab shows that it is possible to create electronic components using biological templates (1,2). The Belcher Lab is currently working on developing M13 bacteriophage templated nanowires and battery electrodes. The development of a biologically templated transistor would complement this work perfectly, as it would potentially enable researchers to create an electronic computer with biologically templated battery, nanowires, user interface (electrochromic device), and CPU (composed of biologically templated transistors). The smallest current transistors are about 100nm long (3). Biologically templated transistors would be able to compete with current transistors because they would be mostly self-assembled, their production would involve only environmentally friendly processes, and they could potentially be only a few times as large as the smallest current transistors.

2. The RNAi pathway has been shown to be active in fighting viral infections by attacking foreign mRNA molecules that have been inserted by virus particles into the cell. It is thought that this was the purpose that led to the evolution of the RNAi pathway. Designing genes to give eukaryotic organisms natural resistance to viruses via the RNAi would be extremely useful for agriculture to prevent virus infections from destroying crops. It has already been shown that designed shRNA sequences have the capability to inhibit viral infection. By encoding genes within the host cells that are expressed as shRNA sequences, we hope to induce the RNAi pathway to be active against specific viruses and grant cells innate immunity. Cells with genes coding for shRNA that have homologous sequences to a virus would hopefully lead to supression of viral activity in infected cells by inactivation of the genetic material and therefore become an effective antiviral tool. Avoiding off-target effects from the designed shRNA is also crucial for the viability of these plant species.

Possible Research Problems and Goals:
Problems:

1. The current cost of CPUs and the non adaptability of conventionally produced transistors are both problems which can be remedied by the creation of biologically templated transistors.

2. It has been difficult to design a method to mitigate the problem of viruses that destroy crop populations. Adding a gene coding for endogenous shRNA specifically targeting viruses that have been identified as a problem is a possible antiviral tool.

Goals:

1. Development of a self-assembling transistor, which is templated on a microorganism such as a bacterial cell or a bacteriophage. The production of these transistors will hopefully mirror the production of the phage templated nanowires we are studying in lab.

2. Development of plants with shRNAs designed to defend against specific viral infections. Genes that encode for candidate shRNAs will be identified and added to specific plant genomes. Ensuring that the shRNA gene works properly with a plant's native RNAi pathway is particularly important.

Previous Efforts:
1. We found no evidence of any previous efforts to construct a biologically templated transistor. A considerable amount of work has been done in the Belcher Lab to create electronic parts templated on modified M13 bacteriophages, but few other microorganisms have been used as templates for electronic parts.

2. The most similar experiment (6) dealt with transiently expressed shRNA that was designed to inhibit the tobacco mosaic virus. The shRNA was not expressed within the plant cells themselves, rather, it was expressed by bacteria transformed with a plasmid coding for the shRNA sequence. The bacteria were then injected into the plants and inhibited viral infection. We aim to design a gene endogenous to the plant cell so that all the cells of the organism will have innate immunity from our target virus.

Resources:
1. Mao C, Solis D, Reiss B, Kottmann S, Sweeney R, Hayhurst A, Georgiou G, Iverson B, Belcher A. Virus-Based Toolkit for the Directed Synthesis of Magnetic and Semiconducting Nanowires. Science(2004); 303(5655): 213-217

2. Nam K, Kim D, Yoo P, Chiang C, Meethong N, Hammond P, Chiang Y, Belcher A. Virus-Enabled Synthesis and Assembly of Nanowires for Lithium Ion Battery Electrodes. Science(2006); 312(5775): 885-888

3. The Wall Street Journal online: http://online.wsj.com/article/SB115095724958887313.html?mod=home_whats_news_us accessed on 16 November 2007

4. M. Nielsen, F. Pedersen, and J. Kjems. Molecular Strategies to Inhibit HIV-1 Replication. Retrovirology (2005) doi: 10.1186/1742-4690-2-10.

5. S.V. Ramesh, A.K. Mishra, S. Praveen. Hairpin RNA-Mediated Strategies for Silencing of Tomato Leaf Curl Virus AC1 and AC4 Genes for Effective Resistance in Plants. Oligonucleotides. 2007, 17(2): 251-257. doi:10.1089/oli.2006.0063.

6. Zhao MM, An DR, Zhao J, Huang GH, He ZH, Chen JY. Transiently expressed short hairpin RNA targeting 126 kDa protein of tobacco mosaic virus interferes with virus infection. Acta Biochim Biophys Sin (Shanghai). (2006) Jan;38(1):22-8.