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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...

Discovery and Study of Microbial Peptide Natural Products

Abstract: 

Discovery and Study of Microbial Peptide Natural Products

Since the discovery of penicillin in the 1920s, natural products have had an unmistakable impact on our health and have inspired us with their intricate chemical structures and fascinating underlying metabolic pathways. Historically, biochemical and genetic studies in these systems have focused on free-living, fast growing terrestrial organisms due to technological and laboratory constraints. However, the past 10-15 years have seen an explosion of new DNA sequencing technologies and molecular biological techniques that have, for the first time, allowed genetic access to more subtle and intricate ecosystems.

This lab's work focuses on the discovery and heterologous expression of pathways and genes involved in the biosynthesis of metabolites from unique microbial sources. The researchers use cutting-edge and classical techniques in biochemistry, microbiology, metagenomics, and mass spectrometry to investigate unconventional peptide-based metabolites and pathways invoking radical-mediated chemistry. MSI resources crucial to this group's success include computing power and software for de novo peptide identification from LC-MS data as well as data management and analysis of sequenced microbial genomes. All in all, this research aims to tackle the exponentially expanding genomic universe for the discovery of new enzymology and therapeutics.

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Group name: 
freeman0

Understanding the Role of Transposable Elements in Maize Abiotic Stress Response

Abstract: 

Understanding the Role of Transposable Elements in Maize Abiotic Stress Response

Abiotic stress, such as extreme temperatures or drought, severely limits agricultural productivity. These researchers have evidence that certain families of transposons can confer stress responsive expression patterns to nearby genes in maize. The first aim of this project is to define the role of transposons in gene expression responses to abiotic stress in several different tissues and genotypes. The focus of the second aim is to determining the mechanism by which transposons influence the stress-responsive expression of nearby genes. The third aim of this project will document natural variation for insertion sites of the transposons that confer stress-responsive gene expression and will attempt to identify protocols to mobilize these elements to generate novel allelic diversity in maize. This project will provide novel understanding of the molecular processes that underlie gene expression responses to abiotic stress. MSI is used for NGS data analysis and other downstream computationally intensive tasks.

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Group name: 
hirschc3

What does job exit status XX mean?

The exit_status attribute reported by "qstat -f <jobId>" can help users identify why a job failed. Successful runs report exit_status=0. Non-zero status (positive or negative) implies job failure, but the exact meaning of exit codes varies by software. For jobs submitted to PBS, negative...

Stratus Protected Data Cloud

MSI is building a local research compute cloud environment called Stratus ( https://stratus.msi.umn.edu ) , which is designed to store and analyze protected data, such as dbGaP. Stratus is a subscription-based infrastructure as a service that enables users to operate within their own self-service...

How do I create a new virtual machine / instance?

The easiest way to boot a VM is through Horizon ( https://stratus.msi.umn.edu ) Go to Project > Compute > Instances and click Launch Instance Horizon provides a Wizard to help you launch VMs. Look for stars (*); those are required fields and can only be set before instance creation! To begin...

Tensorflow

From the Tensorflow website: TensorFlow is an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. TensorFlow was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other...

If you are new to bioinformatics this is the best place to start.

This hands-on tutorial will help a new user understand how to use the the Galaxy platform to analyze NGS data by working though the quality control steps needed for Illumina sequencing data.

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