Elucidating Mechanisms of Fine Genetic Control by a sRNA in Pathogenic Bacterium Salmonella typhimurium

The bacterium Salmonella is a significant cause of food-borne disease. Its pathogenesis depends on the type III secretion systems (T3SSs) that were acquired by horizontal gene transfer; the invasion of Salmonella into the host cells requires appropriate expression of T3SSs. Recent research has identified small non-coding RNAs (sRNAs) as a class of regulators that fine tune gene expression required for bacterial physiology and pathogenesis. Elton will investigate the specific interaction between one of these newly discovered Salmonella sRNA and its predicted candidate targets; he will characterize the interaction between IsrM and its cognate targets, HilE and SopA, and identify the mechanisms of these interactions. The research work on the interaction between this sRNA and its targets will contribute towards a more complete understanding of the molecular coordination of Salmonella pathogenesis.

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Exploring the Mechanism of Protein Scaffolding Toward Improved Metabolic Flux

Metabolic engineering has the potential to provide environmentally friendly routes for the synthesis of a variety of molecules, including therapeutics and biofuels. One way to improve the flux of metabolic pathways is the use of synthetic protein scaffolds that colocalize enzymes in the engineered mevalonate biosynthesis pathway. Susan’s project tests the hypothesis that optimal scaffolds of certain architectures mimic substrate channeling and function by forming large, oligomeric complexes that bring scaffolds into close proximity. Adaptor molecules are synthesized that co-assemble scaffolds to designably control complex size. Mevalonate product titers will be measured using GCMS, and protein colocalization will be verified by fluorescence imaging. The successful engineering of this adaptor strategy can be applied to other pathways due to its modularity.

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Modeling the Impact of Variations in Land Use on Carbon Sequestration Service of Atlantic Forest in São Paulo State, Brazil

Rapid land use transformation worldwide in recent years raises a demand for models that simulate the impacts of different land use policies on the local ecosystems and its services for human well-being. Mio will join a team in Brazil and devise a mathematical model that estimates the impacts of local land use choices on the carbon sequestration abilities of Atlantic Forest. She will integrate the devised model into Multiscale, Integrated Models of Ecosystem Services (MIMES), which collaboratively simulates the impacts of different land use policies on ecosystem services provided by the forest. This research will contribute to the development of effective land management policies that lead to sustainable conservation of Atlantic Forest. Furthermore, identifying the benefits, requirements and limitations of the modeling methods will provide valuable references for future studies.

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Specific Heat Measurements of Silicon Nanowires for Improved Thermoelectrics

Jason’s research group has recently developed the nanocalorimeter, a membrane-based calorimeter which has ten times less addenda heat capacity than any known calorimeter, allowing for the first accurate measurements of nanogram sized samples. With this, Jason proposes to measure the specific heat of silicon nanowires in response to recent thermal transport studies. These studies have found that the thermal conductivity of silicon nanowires decreases with decreasing nanowire diameter. Such a characteristic means silicon nanowires have a big future in clean energy thermoelectric devices. But before we can properly exploit them in technology, their thermal dynamics must be better understood. Directly related to the phonon density of states, specific heat will help Jason explain the decrease in thermal conductivity by investigating phenomena such as phonon confinement and surface vibrational states.

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Molecular Characterization of a piRNA Biogenesis Protein

RNA interference (RNAi) is a rapidly expanding field of research that promises to yield a better understanding of how cells regulate their environments through RNAi mediated gene silencing pathways. Harnessing RNAis transformative properties may prove to be a powerful methodology for developing effective, cell-specific drugs, thus reducing harm and unwanted side effects. Alison’s project involves reconstituting the piRNA biogenesis machinery in vitro; specifically, elucidating the role of the protein, Squash. piRNAs are a recently discovered class of small regulatory RNAs that are thought to facilitate transposon silencing through RNAi, thereby protecting the genome from the deleterious effects of insertional mutagenesis, some of which have been implicated in cancer cell life cycles. Understanding these key mechanisms of gene regulation could radically transform the treatment of many genetically-linked diseases.

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Construction of a Novel, Cryogen-free, Self-contained Dilution Refrigerator

Technologies based on superconducting quantum systems have contributed significantly to the development of high precision magnetic sensors and quantum bits. These experiments require ultra-low temperatures which are achieved by dilution refrigerators. In contrast to conventional dilution refrigerators, which generally require a continuous supply of liquid helium and complex circulation systems, the dilution refrigerator Yu-Dong aims to construct will not use liquid cryogens and mechanical pumps. This will be accomplished by integrating a 2-Kelvin pulse tube cryostat with a self-contained dilution unit prototype from Chase Cryogenics, to further lower the base temperature to 50 milli-Kelvin. This novel dilution refrigerator will be fully computer controlled to optimize cool-down and hold-time, serving as an easy to use, fast cycling system for experiments on superconducting quantum mechanical systems.

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