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Systematics and Evolution of Leptosporangiate Ferns

Abstract: 

Systematics and Evolution of Leptosporangiate Ferns

This work is focused primarily on molecular systematics and phylogenetics of ferns. The researchers are currently undertaking a genome skimming study that will utilize Illumina sequence data collected from across a family of ferns to determine broad patterns of genome structure and repeat content spanning that taxonomic group. Given that there is not yet an assembled and annotated fern genome, this study will illuminate aspects of genome biology in a non-model lineage.

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Group name: 
grusza

Genetic Differences Between Hemp and Marijuana

MSI PIs George Weiblen and M. David Marks , both professors in the Department of Plant Biology , have published research that identifies a gene that distinguishes hemp from marijuana. This research could have implications for future industrial uses of hemp. Currently, legal restrictions affect both...

Engineering in Oncology

Abstract: 

Engineering in Oncology

The microenvironment surrounding carcinoma cells influences cell behavior through complex interactions of biochemical factors, matrix architecture, and matrix mechanical properties. This research focuses on understanding the molecular mechanisms by which the stromal extracellular matrix and stromal cell populations influence epithelial cell behavior in cancer. The researchers are particularly interested in how these factors influence disease progression and resistance to therapeutic intervention in breast and pancreas cancer. They utilize advanced quantitative imaging and cell and matrix mechanics in conjunction with cell and molecular biology techniques and high throughput technologies to gain a quantitative understanding of cancer cells behavior and develop novel technologies and therapeutic strategies for cancer diagnosis and treatment. Within these areas they utilize experimental techniques, modeling of cell behavior and drug transport, and analysis of large genomic, proteomic, and high-metric-content imaging datasets. MSI resources are used for analysis and to process large datasets and complex models.

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Group name: 
provenza

Study of Copper Oxidoreductase Redox Potentials

Abstract: 

Study of Copper Oxidoreductase Redox Potentials

This group is interested in structural factors that influence and tune reduction potentials in metalloproteins, specifically copper oxidoreductase enzymes. They have determined a series of protein crystal structures of mutants of the small Cu protein azurin, which have varied experimental reduction potentials. They are computationally analyzing the environment around the Cu centers in each of these crystal structures, looking for differences such as dipole moments, local charges, solvent content, etc. In collaboration with a colleague, Assistant Professor Alessandro Cembran, this group is beginning with classical molecular dynamics simulations on the crystal structures, using programs such as GROMACS, and analyze electrostatic differences between mutants and will later likely progress to higher level QM/MM simulations using programs such as Gaussian. 

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Group name: 
berrys0

Total RNA Expression Profiling of Extracellular Vesicles

Abstract: 

Total RNA Expression Profiling of Extracellular Vesicles

Extracellular vesicles (EVs) are small membranous structures that are between 50 and 1000 nm in diameter and are present in extracellular spaces and bodily fluids. They are formed from cells in vivo and in vitro from either exocytosis of endosomal vesicles or from plasma membrane blebbing. While initial observations assumed the EVs were cellular waste or debris, evidence now indicates that EVs are part of a signaling mechanism that conducts molecular messages between cells either locally or remotely (long distances). Major signaling molecules in EVs are micro RNAs and mRNAs. In this study EVs are isolated from animal blood or cultured cell media. The isolated EVs are than extracted to collect their total RNA content. The total RNA is used to construct a library and the library is subjected to next generation sequencing. The reads will be quantified, annotated and analyzed.

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Group name: 
drewes

Metabolomics and Stable Isotope Labeling Methodologies for the Study of Chemical Communication in Plants

Abstract: 

Metabolics and Stable Isotope Labeling Methodologies for the Study of Chemical Communication in Plants

Plants synthesize a wide variety of chemicals called secondary metabolites in response to environmental triggers or to mediate specific behaviors from other organisms. Very little is known about how the synthesis of these metabolites is regulated or how their environmental triggers are sensed. The Hegeman laboratory uses and develops high-throughput mass spectrometry-based analyses to provide broad-based measurements of metabolites. They are also involved in developing new methodologies in metabolomics that utilize whole-organism stable isotopic labeling strategies to improve data quality and information content. These analyses will be used to provide global models of metabolism within a biological system that can provide novel insights into molecular phenomena. The researchers use these metabolomics approaches to understand the regulation of secondary metabolite production in response to environmental cues. 

This PI’s research was featured in MSI Research Spotlights in February 2015 and November 2015.

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Group name: 
hegemana

Call for Proposals - Allocations on Blue Waters HPC System

The Great Lakes Consortium for Petascale Computation (GLCPC) has issued a Call for Proposals for allocations on the Blue Waters system. The Call for Proposals can be found on the GLCPC website . Proposals should focus on the scale and unique capabilities of the Blue Waters system. Projects that...

Scratch Storage

MSI provides large capacity and high performance temporary storage to be used while applications are running on the supercomputer. Depending on the system, scratch storage may be a set-aside area of primary storage (global scratch), or may consist of separate storage attached via fast data links...

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