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Fungal Gut Microbiomes

Abstract: 
<h3 class="red">Fungal Gut Microbiomes</h3><p>The Gale lab studies the fungal gut microbiome in a variety of human and mouse subjects. Fungal sequencing is performed by the <a href="http://www.health.umn.edu/research/resources-researchers/genomics-center">University of Minnesota Genomics Center</a> using a next-generation sequencer from Illumina. Data generated by sequencing is analyzed using MSI&#39;s HPC systems due to the massive amounts of output from the sequencing experiments.&nbsp;</p><p>This PI&rsquo;s research was featured in an <a href="https://www.msi.umn.edu/content/fungal-microbiome-infants">MSI Research Spotlight</a> in April 2015.</p><p>Return to this PI&rsquo;s <a href="https://www.msi.umn.edu/pi/56212e54025dd4e97ae4a1bccbb126e9/45995">main page</a>.</p>
Group name: 
galeca

Systematics and Evolution of Leptosporangiate Ferns

Abstract: 
<h3 class="red">Systematics and Evolution of Leptosporangiate Ferns</h3><p><span style="background-color: rgb(255, 255, 255);">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.</span></p><p><span style="background-color: rgb(255, 255, 255);">Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/a3fff1da0c973cd375d82286e58f9ecc/10967">main page</a>.</span></p>
Group name: 
grusza

Sterile Neutrinos and Supernovae

Abstract: 
<h4>Sterile Neutrinos and Supernovae</h4><div class="node-column-original" style="font-size: 14px; background-color: rgb(255, 255, 255); color: rgb(51, 51, 51);"><div class="view view-access-requests view-id-access_requests view-display-id-by_group_name view-dom-id-15c7a9afe37f149301689285d0526d34" style="font-size: 14px;"><div class="view-content" style="font-size: 14px;"><div class="views-row views-row-1" style="font-size: 14px;"><p class="views-field views-field-abstract" style="font-size: 14px;"><span class="field-content" style="font-size: 14px;">Neutrinos are neutral particles that only interact with other particles through the weak interaction. In the Standard Model of particle physics, there exist only three different kinds of neutrinos carrying three different weak charges. Recently, several neutrino experiments have pointed to an additional kind of neutrino that does not participate in weak interaction: the sterile neutrino. Although they do not interact directly with other particles, the mixing between sterile and weakly-interacting neutrinos allows experiments to discover their possible existence, which if confirmed, will be the smoking gun of physics beyond the Standard Model. These researchers have shown that the existence of sterile neutrinos indicated by reactor neutrino experiments could have potentially strong impact on the explosion and the element formation in supernovae, which are among the most energetic astrophysical events in our universe. They are using MSI to further investigate this problem in a self-consistent manner. Since they need to couple the calculation of neutrino flavor evolution with the hydrodynamical calculations of supernovae and their ejecta, this demands the use of high performance computing. The researchers expect the result of this study will allow them to&nbsp;</span><span style="font-size: 14px; background-color: rgb(255, 255, 255); line-height: 1.5;">better</span><span style="font-size: 14px; background-color: rgb(255, 255, 255); line-height: 1.5;">understand the role of sterile neutrinos in supernovae and to constrain their fundamental properties.</span></p></div></div></div></div><p>&nbsp;</p>
Group name: 
qianyz

Role of Staphylococcal Toxins in Cardiac Dysfunction in CA-MRSA Sepsis

Abstract: 
<h4>Role of Staphylococcal Toxins in Cardiac Dysfunction in CA-MRSA Sepsis</h4><div class="node-column-original" style="font-size: 14px; background-color: rgb(255, 255, 255); color: rgb(51, 51, 51);"><div class="view view-access-requests view-id-access_requests view-display-id-by_group_name view-dom-id-9ef6c25a030c15897f2ecac7f10ff80b" style="font-size: 14px;"><div class="view-content" style="font-size: 14px;"><div class="views-row views-row-1" style="font-size: 14px;"><p class="views-field views-field-abstract" style="font-size: 14px;"><span class="field-content" style="font-size: 14px;"><span style="font-size: 14px; background-color: rgb(255, 255, 255); line-height: 1.5;">Community-acquired methicillin-resistant <em>Staphylococcus aureus</em> (CA-MRSA) is responsible for a growing share of staphylococcal infections in pediatric patients in the United States. The USA300 strains of CA-MRSA have been associated with severe infections including sepsis associated with high rates of morbidity and mortality in previously healthy pediatric patients. The mechanisms causing cardiac dysfunction in sepsis, including in CA-MRSA sepsis, are not well defined but appear to involve pro-inflammatory cytokines as well as changes in genes regulating contractile function and ion channels. There is limited information published on cardiac dysfunction in staphylococcal sepsis, especially in CA-MRSA sepsis. USA300 CA-MRSA produced numerous virulence factors. Superantigens (represented by the novel superantigen Selx in USA300) and alpha toxin are associated with cardiac dysfunction in animal models. These researchers are testing the hypothesis that Selx and alpha-toxin play a significant role in causing cardiac dysfunction in CA-MRSA sepsis by affecting regulation of genes for inflammatory mediators, contractile proteins, and ion channel function. They use microarray technology to analyze changes in regulation of gene networks involved in cardiac function</span>.</span></p><p class="views-field views-field-abstract" style="font-size: 14px;"><span style="font-size: 14px; line-height: 1.5;">Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/89f41ccf8116fb81062635a3e88d9799/10683">main page</a>.</span></p></div></div></div></div><p>&nbsp;</p>
Group name: 
humej

Collaborative Next-Generation Sequencing of Equine Neuromuscular Diseases

Abstract: 
<h4>Collaborative Next-Generation Sequencing of Equine Neuromuscular Diseases</h4><div class="node-column-original" style="font-size: 14px; background-color: rgb(255, 255, 255); color: rgb(51, 51, 51);"><div class="view view-access-requests view-id-access_requests view-display-id-by_group_name view-dom-id-1f9ec6d512610d4a9ea42a675fd1332e" style="font-size: 14px;"><div class="view-content" style="font-size: 14px;"><div class="views-row views-row-1" style="font-size: 14px;"><p class="views-field views-field-abstract" style="font-size: 14px;"><span class="field-content" style="font-size: 14px;">In collaboration with Professor <a href="https://www.msi.umn.edu/pi/470711c0eee2ba32f015ac0469b30f4e/10477">Stephanie Valberg</a>, this researcher is&nbsp;<span style="font-size: 14px; background-color: rgb(255, 255, 255);">analyzing NGS data from horses with inherited neuromuscular diseases</span>. The research makes use of the&nbsp;<a href="https://galaxy.msi.umn.edu">Galaxy</a> interface as well as access through MSI labs&nbsp;<span style="font-size: 14px; background-color: rgb(255, 255, 255);">to perform quality control on fastq files, align reads to the reference sequence, and perform variant detection analyses on DNASeq data files. Other collaborative research involves RNASeq data analysis</span>.</span></p><p class="views-field views-field-abstract" style="font-size: 14px;"><span style="font-size: 14px; line-height: 1.5;">A bibliography of this group&rsquo;s publications is attached.</span></p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/4a3b73053def64747f40ef51b8536e17/10666">main page</a>.</p><p>&nbsp;</p></div></div></div></div><p>&nbsp;</p>
Group name: 
finnoc0
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Multiscale Design of Hard and High Temperature Resistant Coatings

Abstract: 
<h3 class="red">Multiscale Design of Hard and High Temperature Resistant Coatings</h3><p>This project involves an interdisciplinary effort to conduct multiscale design of hard and high temperature resistant (Si,Zr)-B-C-N coatings which are thermally stable and oxidation resistant for high temperature (&gt;1500 &deg;C) applications. The project couples multiscale computations and experiment to merge the high-temperature oxidation resistant properties of Si-B-C-N and high hardness properties of Zr-B-C-N systems. The predictive effort spans from atomistic to multiscale distinct element method simulations to formulate solid predictions of the optimized compositions. These predictions will provide critical guidance for synthesizing coatings with targeted properties. These researchers expect that in these new coatings, the desirable properties will coexist, resulting in a new generation of protective layers.</p><p>This research is far-reaching as it can enable new concepts for protective coatings and the development of a new multiscale tool to predict materials&#39; response. Molecular dynamics investigation will address the fundamental issue of combining desirable properties by varying chemical composition and structure. The application of the distinct element modeling down to the nanoscale represents a new powerful tool to simulate the global behavior, allowing the design of future materials at large. The focus of this research - the discovery of new coatings working under extreme conditions - can find application in multitude of critical components such as turbine blades, reusable launch vehicles, hypersonic vehicles, and thermal barrier applications.</p><p>Research Spotlights about this group&#39;s work appeared on the MSI website in <a href="https://www.msi.umn.edu/content/modeling-properties-graphene">August 2014</a>&nbsp;and <a href="https://www.msi.umn.edu/content/understanding-effects-dislocations-thermal-properties-materials">March 2015</a>.</p><p>Return to this PI&rsquo;s <a href="https://www.msi.umn.edu/pi/030e6829662dfd0ba236adce758ba777/42109">main page</a>.</p>
Group name: 
dumitric

Molecular Evolution of Vertebrates

Abstract: 
<h3 class="red">Molecular Evolution of Vertebrates</h3><p>This lab has several ongoing projects:</p><ul><li>A large-scale population genomics effort using Illumina resequencing in the Astyanax cavefish shotgun genomes. Cavefish have distinct phenotypes from surface conspecifics and are emerging models for research on obesity, retinal degeneration, and sleep disorders. These researchers are assaying for convergent and divergent evolutionary signatures across two separate evolutionary orgins of the cavefish and examining candidate genes. They have found some promising results, but will continue building this project over the next one-two years by adding populations and using a PacBio based reference assembly (currently they are using an Illumina-based reference assembly).</li><li>Investigation of how pathways evolved between reptiles and mammals. The researchers have completed a deep-time selection analyses on the insulin signalling network (published in <em>PNAS</em> in 2015). They found evidence of potential subfunctionalization between key proteins at the top of the insulin signalling network. The researchers are following up that project with an analysis of the how P53 pathway, a major cancer and cell cycle regulator, has evolved in amniotes. Another follow-up project addresses how uncoupling proteins (involved in thermogenesis) have evolved.</li><li>A variety of other smaller projects including population genomics of parapatric snakes with vastly different life histories and processing RADseq genetic maps.</li></ul><p>This PI&rsquo;s research was featured in MSI Research Spotlights in <a href="https://www.msi.umn.edu/content/blind-cavefish-genome">November 2014</a> and <a href="https://www.msi.umn.edu/content/new-data-storage-option-msi-researchers">March 2015</a>.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/b909667be1d08c45cc08f5f2ff8ba4a7/10319">main page</a>.</p>
Group name: 
mcgaughs

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...

Elucidating the Molecular Mechanisms That Modulate the Anti-Cancer Immune Response and Control Malignant Transformation and Progression in Cancer

Abstract: 
<h3 class="red">Elucidating the Molecular Mechanisms That Modulate the Anti-Cancer Immune Response and Control Malignant Transformation and Progression in Cancer</h3><p>This research program can be broadly classified into four major complementary areas that intersect in each of the lab&rsquo;s primary research projects:</p><ul><li>Understanding the mechanism of malignant transformation and progression in colon cancer.</li><li>Elucidating the molecular mechanisms that modulate the anti-cancer immune response:.</li><li>Development of novel analysis tools and strategies to understand cancer gene regulation.</li><li>Identification and development of novel biomarkers and therapeutics in osteosarcoma.</li></ul><p>The group has made significant advances in projects related to these areas, including the discovery of mechanisms that trigger malignant transformation and progression in colon cancer; human sarcoma pathobiology microRNA gene networks in cancer; and mechanisms that trigger osteosarcoma development and progression.</p><p>A Research Spotlight about this PI&#39;s work appeared in <a href="https://www.msi.umn.edu/content/genetic-differences-osteosarcoma-subtypes">January 2016</a>.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/09826f433440ef43c40f90562b097d0a/10034">main page</a>.</p>
Group name: 
subraman

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