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Antimicrobial Peptides and Autoimmune Disease

Abstract: 

Antimicrobial Peptides and Autoimmune Disease

The Sjögren’s Syndrome Knowledge Base (SSKB) is a resource for Sjögren’s syndrome research. The foundation for SSKB is a database of genes and proteins associated with Sjögren’s syndrome extracted from PubMed. The foundational database was established using the text-mining program EBIMed to query the Pubmed database, using the search term "Sjogren's Syndrome" restricted to "MeshHeadingsList."

The initial search in 2007 resulted in a selection of 7,733 abstracts and 1,293 potential genes/proteins. The abstracts were manually evaluated to remove duplicates and false-positives, resulting in a preliminary database of about 900 protein names and associated genes. In the case of older publications, where gene names were not readily identifiable, gene names were assigned based on in depth evaluation of the protein name context and available gene data in public databases, including Entrez and Uniprot. The data is continually updated and manually annotated to include new publications and data relating to the genes in the SSKB.

In a second project, microbiome data are collected by 16S rRNA sequencing of microbial samples from mouse and human anatomical sites. Data storage is requested for large data sets. Analysis is conducted in collaboration with the laboratory of Dan Knights (Computer Science and Engineering).

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Group name: 
gorrsu

Enzymology and Biotechnology of Protein Prenylation

Abstract: 

Enzymology and Biotechnology of Protein Prenylation

Protein prenylation is an irreversible covalent post-translational modification found in all eukaryotic cells, comprising of farnesylation and geranylgeranylation. Three prenyltransferase enzymes catalyze this modification. This three-step process increases protein hydrophobicity, and often leads to plasma membrane association. Prenylation serves as the first critical step for membrane targeting and binding, as well as mediating protein-protein interactions of a large number of Ras proteins; heterotrimeric G-proteins also require prenylation for activity.Significant interest in studying protein prenylation originally stemmed from the finding that this modification was necessary to maintain malignant activity of oncogenic Ras proteins although now it is known that prenylation is important in a wide ranges of diseases. These researchers are using computer-based methods for three subprojects within this area. They include:

  • Design of caging groups used to mask the activity of substrates and inhibitors of protein prenylation
  • Bioinformatic analysis of proteomic data obtained using probes that allow selective detection of prenylated proteins
  • Modeling of prenyltransferase structures to design mutations that alter substrate specificity

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Group name: 
distefan

Phylogenetic Analysis of Trait Evolution

Abstract: 

Phylogenetic Analysis of Trait Evolution

These researchers study the evolution of traits that influence chances of speciation and extinction. Plant mating system is one such trait, because it strongly affects population sizes and distributions of genetic diversity. Geographic range is another such trait because geologic, climatic, and biotic conditions all affect population size and subdivision. Other traits are often associated with these, and it can be challenging to identify the particular traits or trait combinations that most directly affect speciation and extinction.

This work typically involves two phases of analysis, each of which can be computationally intensive for groups of more than, say, a thousand species. First is constructing a phylogeny of living species from DNA sequence data. Second is fitting models of trait evolution, speciation, and extinction to those phylogenies. Such analyses are easily parallelized, especially when conducted in a Bayesian statistical framework, and so the researchers can readily make use of MSI's cluster resources.

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Group name: 
eeg

Functional Genomics

Abstract: 

Functional Genomics

These researchers have five current projects using MSI resources:

  • Mutant mapping studies: Using bulk segregate analysis, useful soybean mutant phenotypes will undergo mapping studies to restrict causative genes to a region of a chromosome. Whole-genome sequencing (WGS) will be generated and analyzed on wild-type and mutant bulks for each phenotype of interest.
  • Comparison of mutation rates: This project is looking at change in mutation rates between standing, irradiated, and transformed genetic variation using soybean WGS. The group will also be looking at differences in large structural variants between these populations as well as various population genetics metrics.
  • Creation and application of soybean co-expression networks: Using publically available soybean RNA-seq expression data, the researchers will generate expression values and build a general co-expression network. Using this network, they will then integrate it with differential expression studies for interesting phenotypes to generate a list of candidate genes.
  • Exploring the soybean germplasm collection: This project uses publicly available climate, soil, and genotypic data to run a mixed linear model of association. With multiple populations and 80 different environmental phenotypes available this will result in large computational use.
  • RNA seq of F1 hybrids: This project explores the soybean transcriptome and how it is affected by parentage and copy number variation. This involves analysis of both WGS and RNA-seq data.

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Group name: 
stuparr

Biomolecular Simulations of Soluble and Membrane-Bound Complexes

Abstract: 

Biomolecular Simulations of Soluble and Membrane-Bound Complexes

This research focuses on the investigation of the molecular mechanisms that regulate cell signaling in multicellular organisms. Signal specificity is encoded into the 3D structure of proteins that transfer specific information from the cell surface to the nucleus, leading to changes in gene expression and cellular biochemistry. This lab studies these signaling processes examining how aberrant protein interactions and structural variation may lead to pathophysiologies of calcium signaling in cardiac and skeletal muscle. Calcium is a central messenger for contractility, and dysfunctional calcium signal transduction is linked to several pathologies including heart failure and muscular dystrophy. There has been a continuous effort to develop small molecules and protein therapies to ameliorate these pathological conditions. To elucidate the biochemical and structural bases for these processes, these researchers determine the 3D structures of protein complexes that are involved in calcium trafficking. Toward this end, the group is developing new structural biology approaches using Nuclear Magnetic Resonance (NMR) spectroscopy to obtain structural information on these large macromolecular complexes. They also study two important post-translational modifications central to calcium signal transduction and protein recognition: phosphorylation and myristoylation. Computational approaches are fundamental to understanding and interpreting the conformational dynamics information obtained from NMR studies. Toward this goal, the researchers have established a strong collaboration with the group of Jiali Gao (Chemistry). The overall goal of this research is to decipher the mechanisms underlying cell signaling and develop new frameworks for innovative therapeutic approaches.

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Group name: 
vegliag

Snapshot Serengeti: Camera Traps to Monitor Biodiversity in Serengeti National Park, TZ

Abstract: 

Snapshot Serengeti: Camera Traps to Monitor Biodiversity in Serengeti National Park, TZ

Camera traps can be used to address large-scale questions in community ecology by providing systematic data on an array of wide-ranging species. These researchers deployed 225 camera traps across 1,125 km2 in Serengeti National Park, Tanzania, to evaluate spatial and temporal inter-species dynamics. The cameras have operated continuously since 2010 and had accumulated 99,241 camera-trap days and produced 1.2 million sets of pictures by 2013. Members of the general public classified the images via the citizen-science website Snapshot Serengeti. Multiple users viewed each image and recorded the species, number of individuals, associated behaviours, and presence of young. Over 28,000 registered users contributed 10.8 million classifications. The consensus classifications and raw imagery provide an unparalleled opportunity to investigate multi-species dynamics in an intact ecosystem and a valuable resource for machine-learning and computer-vision research.

This research was featured in a Research Spotlight on the MSI website in July 2015. 

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Group name: 
packerc

Treatment for Clostridium difficile Infections

MSI PIs Dan Knights ( Computer Science and Engineering - College of Science and Engineering ) and Michael Sadowsky ( Soil, Water, and Climate - College of Food, Agricultural, and Natural Resource Sciences ), are co-authors on a recent study supporting the value of fecal transplantation for the...

Mechanistic Investigation of Allylic Azides

Abstract: 

Mechanistic Investigation of Allylic Azides

Allylic azides have been known to undergo spontaneous rearrangement to form an equilibrating mixture of branched and linear azides. Although the mechanism for such an event has been speculated in the past, detailed investigations have not been done yet to elucidate key intermediates or favorable energetic pathways. Experimentally, it has been shown that substituents on the allylic azide can affect the reaction equilibrium and subsequently the ratio of the equilibrating mixture. This equilibrium may also be influenced by interactions like hydrogen bonding of the substrate, however no experimental evidence substantiates these claims.

Computational studies can go a long way in gaining mechanistic insights of these reactions by identifying favorable transition states and/or reactive intermediates and role of various non-covalent binding events. These researchers envision that mechanistic analysis of the allylic azide rearrangement will provide insights for optimization of current reaction conditions. With these insights, the allylic azides can be synthetically converted to value added precious materials like chiral amines, which are important moieties in various substances like drugs, natural products, and more.

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Group name: 
topczews

Analysis of Gene Expression in Retinal Mononuclear Cells

Abstract: 

Analysis of Gene Expression in Retinal Mononuclear Cells

This lab is interested in the origin and nature of mononuclear cells in the retina. These cells are critical for the immune homeostasis of the eye, and are critical in determining and controlling appropriate immune responses to injury and inflammation. Many retinal mononuclear cells are phenotypically indistinguishable, thus making their exact origin and function hard to determine. These researchers are studying the transcription profile of individual cells to distinguish various mononuclear cells and to determine their exact origin and function. Recently, a paper was published (Cell 161:1214, 2015) cataloging all transcripts (the transcriptome) from 44,000 individual retinal cells and then determining cell type based on transcript patterns. These researchers are interested in mining this data to develop a set(s) of genes that can aid us in identification and distinguishing retinal mononuclear cells. Computing resources at MSI will be used to set up and analyze the large matrices (digitized gene expression files) associated with looking at the transcripts from each cell.

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Group name: 
gregerso

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...

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