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Engineering in Oncology

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<h3 class="red">Engineering in Oncology</h3><p>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.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/f741596781dd50899c4affba0a07d26f/10585">main page</a>.</p><p>&nbsp;</p>
Group name: 
provenza

Identifying an Insulin-Like Growth Factor Driven Metastasis Signature in Breast Cancer

Abstract: 
<h3 class="red">Identifying an Insulin-like Growth Factor Driven Metastasis Signature in Breast Cancer</h3><p>Insulin-like growth factors signaling through the type IGF receptor (IGF1R) regulate proliferation, metastasis, and metabolism of breast cancers. In triple negative breast cancer (TNBC) IGF1R regulates metastasis. In TNBC, inhibition of IGF1R blocks metastasis but not tumor growth at the primary site. In ER+ cell lines IGF-I regulates tumor growth in the primary site. Drugs targeting IGF1R are being tested in clinical trials but no biomarkers of IGF driven tumors have been identified. This project seeks to develop an IGF driven metastasis signature in triple negative breast cancers that could potentially be used to identify patients with TNBC that may benefit from inhibition of the IGF system. To generate the signature two TNBC cell lines and one ER+ line were treated with the ligand IGF-I, an inhibitory Ab, or IGF-I and antibody together for 4 and 24h. RNA was isolated and samples were subjected to RNA sequencing using 100 bp paired end runs on the HiSeq 2000 through the <a href="http://centers.umn.edu/content/genomics-center">University of Minnesota Genomics Center</a>.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/db1895df3cf2d0dff96dc1a4d2f881c1/10126">main page</a>.</p>
Group name: 
sachdevd

For Healthcare: Interactive Simulation and Modeling, and More

Abstract: 
<h3 class="red">For Healthcare: Interactive Simulation and Modeling, and More</h3><p>These research and development efforts are focused on interactive simulation and modeling methods for healthcare interventions. As a unique interdisciplinary team in the UMN Medical School&rsquo;s simulation programs, these researchers have been working with medical device companies and healthcare providers to develop and license out technology innovations as new medical training tools or curricula. Their research outcomes include new virtual reality simulators that make surgical training more efficient, and consequently enhance patient safety through simulation based training. Physicians and medical students worldwide are now using instruments made at the University to exercise and perfect their clinical techniques.</p><p>Ongoing work include studies in new simulation and visualization algorithms, motion tracking, sensor fusion, machine learning and smart tools for medical applications. As virtual reality, augmented reality, or mixed reality are experiencing promising evolutions in aspects of usability and cost-efficiency, these researchers look forward to integrating new research ideas and technology gizmos into useful instruments addressing actual needs in healthcare practices.</p><p>A Research Spotlight about this PI&#39;s work appeared in <a href="https://www.msi.umn.edu/content/computer-simulations-hydraulic-jumps">March 2016</a>.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/53e1978b4960a020da55906974cf56fd/10719">main page</a>.</p>
Group name: 
medicalsim

Wheat and Intermediate Wheatgrass Breeding and Genetics

Abstract: 
<h3 class="red">Wheat and Intermediate Wheatgrass Breeding and Genetics</h3><p>These researchers are mapping genes in wheat and intermediate wheatgrass that control important traits, including disease resistance and grain quality. Segregated populations of 100-200 lines, Association Mapping panels, and breeding lines for genomic selection are phenotyped in appropriate environments, and populated with several hundred to several thousand DNA markers to identify DNA markers associated with genes or QTLs affecting the trait or develop genomic selection models. Mapping populations currently active in the lab include those for: leaf rust resistance, stem rust resistance, <em>Fusarium</em> head blight resistance, and grain end-use quality. MSI resources used include mapping and genotyping software and storage space for data.</p><p>A Research Spotlight about this PI&#39;s work appeared in <a href="/content/identifying-rust-resistance-genes-wheat">June 2016</a>.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/77d053caf0a127d23b652a945eab0d20/11453">main page</a>.</p>
Group name: 
janderso

Structural and Molecular Basis of Human Diseases

Abstract: 
<h3 class="red">Structural and Molecular Basis of Human Diseases</h3><p>This research focuses on the structural and molecular basis of human diseases including virus infections, cancer, and abnormal blood pressure. One line of research examines the invasion mechanisms of viruses. The researchers investigate the structures and functions of virus-surface proteins that mediate receptor recognition and cell entry of viruses. A second line of research explores the structural basis for cancer and abnormal blood pressure. Specifically, the group investigates the structures and functions of mammalian-cell-surface enzymes that are critical for tumor cell growth and blood pressure regulation. Based on these structural studies, the researchers further develop novel therapy strategies to treat human diseases. Their research tools include X-ray crystallography, electron microscopy, protein biochemistry, molecular virology, and vaccine and drug designs.</p><p>This research was featured in a <a href="https://www.msi.umn.edu/content/targeting-drugs-tumors">Research Spotlight</a>&nbsp;on the MSI website in June 2015.&nbsp;</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/ba7a93a63506404bf82efd56bd4897a4/10768">main page</a>.</p>
Group name: 
lifang

Design of Selective Histone Deacetylase (HDAC) Inhibitors

Abstract: 
<h3 class="red">Design of Selective Histone Deacetylase (HDAC) Inhibitors</h3><p>Applying the principles of fragment- and structure-based drug design, this project investigates novel structural templates for the discovery of selective HDAC inhibitors. The strategy is to design, synthesize, and screen small fragments with limited structural features. Preliminary biological evaluations of these fragments allow for an expeditious exploration of diverse chemical structures, and provide useful information about the protein-ligand interactions. Subsequent chemical modifications, guided by the observed structure-activity relationship (SAR) and computational modeling, are aimed to optimize the potency and potential selectivity among HDAC isoforms.</p><p>This research was featured in an <a href="https://www.msi.umn.edu/content/creating-compounds-treat-disease">MSI Research Spotlight</a> in January 2015.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/265a3ca425f5ade5d8193e08bebf9e66/10177">main page</a>.</p>
Group name: 
chenlq

Functional Genomics of Enterococcus faecalis

Abstract: 
<h3 class="red">Functional Genomics of <em>Enterococcus faecalis</em></h3><p>The Dunny lab studies the genetic basis for the ability of the bacterium <em>Enterococcus faecalis</em> to colonize the intestinal tract as a harmless commensal organism and to cause opportunistic infection in persons with impaired immunity or who have been heavily treated with antibiotics. The researchers make extensive use of Illumina sequencing for analyzing gene expression, comparing competitive fitness of large numbers of mutants, and for identification of spontaneous changes in genome sequences under selective pressures.</p><p>A <a href="https://www.msi.umn.edu/content/understanding-pathogens-and-biofilms">Research Spotlight</a> about this work appeared on the MSI website in October 2015.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/3050b703e1589c66318f568191773d1f/56600">main page</a>.</p>
Group name: 
dunnearh

Genomic Study of Kidney Transplant Recipients

Abstract: 
<h3 class="red">Genomic Study of Kidney Transplant Recipients</h3><p>These researchers have begun to study whether genetic variants are, in part, responsible for the differing outcomes of kidney transplant recipients treated with similar immunosuppressive protocols. Their central hypotheses are that genetic variation is associated with kidney transplant outcome (i.e., acute rejection, chronic graft dysfunction, and graft loss) and immunosuppressive drug toxicity. The researchers will carry out genome-wide association analysis for such purpose. They use MSI resources to store the genotype data, and perform association tests between genotypes and various endpoints in kidney transplantation. They are also carrying out genotype imputation to obtain best guess/dosage for un-genotyped variants using public reference panels (1000 Genomes project), which can be used to perform meta-analysis with results from other research groups to increase the power of detecting underlying genetic variants.</p><p>A Research Spotlight about this PI&#39;s work appeared in <a href="https://www.msi.umn.edu/content/finding-genetic-markers-transplant-rejection">February 2016</a>.</p><p>Return to this PI&rsquo;s <a href="https://www.msi.umn.edu/pi/a460eb911d98001d0dba100a3006b7aa/10151">main page</a>.</p><p>&nbsp;</p>
Group name: 
guanwh

Large Scale Simulations for Virtual Worlds

Abstract: 
<h4>Large Scale Simulations for Virtual Worlds</h4><p>Large-scale virtual worlds are becoming increasingly common, with a wide range of applications including games, virtual reality, training environments, egress analysis, and predictive simulation. For many of these applications, very large-scale simulations are needed to achieve their full potential, but the scale of the simulation is strongly limited by computational resources. This project seeks to investigate approaches to parallelizing the key algorithms needed to create realistic, large-scale virtual environments. By developing parallel-friendly algorithms, these researchers aim to be able to more efficiently use available computational resources, and thereby create larger, more realistic virtual environments.&nbsp;</p><p>A bibliography of this group&rsquo;s publications is attached.&nbsp;<span style="font-size: 14px; line-height: 1.5;">This research was featured in an <a href="https://www.msi.umn.edu/content/simulations-interacting-objects">MSI Research Spotlight</a> in September 2014.</span></p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/d8387775b6eb718d82cf12bfcc693d9c/10554">main page</a>.</p><p>&nbsp;</p>
Group name: 
guys
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Metallic Nanostructures for Biosensing and Photonics

Abstract: 
<h3 class="red">Metallic Nanostructures for Biosensing and Photonics</h3><p>This research group focuses on the interaction of light with metallic nanostructures for the use of biosensing, metamaterials, and spectroscopy. By using microfabrication techniques, they fabricate small metallic structures that are resonant with light to create extremely high local fields. This large field enhancement enables very strong interactions with matter, even individual molecules, for the use of chemical identification, imaging, and sensing, that would not be available to other techniques. Various ongoing projects include the development of novel near-field imaging probes, lipid bilayer and raft formation for analogs to cellular systems, high-performance design of devices for chemical diagnostics and sensing, and advanced metamatericals for light trapping in photonics. In order to design and study these devices, numerical modeling is used to simulate these structures and their complex coupling with light at the nanoscale.</p><p>A Research Spotlight about this PI&#39;s work appeared in <a href="/content/new-method-detect-single-molecules">May 2016</a>.</p><p>Return to this PI&rsquo;s <a href="https://www.msi.umn.edu/pi/4b0567936b799fdd79e9dc8878a75d43/41332">main page</a>.</p>
Group name: 
ohsh

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