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Partek Genomics Suite

Partek Genomics Suite (Partek GS) is a software suite of statistics and interactive data visualization designed to extract biological signals from noisy data. Partek GS is able to support microarray and next generation sequencing technologies including DGE and gene expression, RNA-seq and alternative splicing, copy number and association, ChIP-chip, ChIP-seq, and microRNA.

SGA - String Graph Assembler

From the SGA GitHub repository: Overview SGA implements a set of assembly algorithms based on the FM-index. As the FM-index is a compressed data structure, the algorithms are very memory efficient. An SGA assembly has three distinct phases. The first phase corrects base calling errors in the reads. The second phase assembles contigs from the corrected reads. The third phase uses paired end and/or mate pair data to build scaffolds from the contigs. Example real-data assemblies can be found here. Error Correction The first stage of the assembly. An FM-index of the sequence reads is constructed...

Modeling Hydrogen Bond Arrays

The research group of Professor Steven Kass ( MSI Fellow , Chemistry ) uses MSI resources in their investigations into hydrogen bond networks. The goal of this research is to understand enzyme catalysis and develop hydrogen bond catalysts, novel acids and bases, and molecular anion receptors. By...

Investigating the Maize Transcriptome

In the course of the history of agriculture, humans have tried to change the properties of the crops they raise. Maize (corn) is a very valuable and widely grown crop, and researchers are able to trace how modern maize has been developed from its wild ancestor, a plant called teosinte ( Zea mays...

Modeling Polymer Structures and Dynamics

Polymers, which many people think refer only to plastic, are actually a large group of natural and man-made materials. They have many uses in industry and as consumer products. Some of these include the super-absorbant polymers used in disposable diapers, the heat-stable materials used for non-...

Investigating Proteins With Crystallography

The research group of Professor Carrie Wilmot in the Department of Biochemistry, Molecular Biology, and Biophysics concentrates on understanding the synthesis and function of novel organic, organometallic, and metal-ion cofactors in proteins. (A cofactor is a chemically reactive protein...

Visualizing Viruses

In the ongoing study of viruses, researchers are using powerful computer resources to create visualizations of virus structures. MSI Principal Investigator Wei Zhang , a research assistant professor in the Department of Diagnostic and Biological Sciences ( School of Dentistry ), is investigating...

Molecular Evolution of MyTH-FERM Myosins


Molecular Evolution of MyTH-FERM Myosins

Cell motility, the movement of cells through their environment, is of fundamental importance in biology and particularly in multicellular animals as cells must migrate through the devleoping organism to form specialized tissues. The Titus group studies myosins, a class of motor proteins with deep evolutionary roots that control cell shape, motility, and migration in both animals and Dictyostelium (Dicty), a social amoeba. Dicty is a unicellular organism that feeds on soil bacteria and develops into a multicellular aggregate, and is a model for cell motility and migration. These researchers have identified two MyTH4-FERM (MF) myosins in Dicty. MF myosins contain both a motor and a binding module, the MyTH4-FERM domain, allowing the motor to generate force across the cytoskeleton and receptors at the cell membrane. MF myosins are a diverse family of motors found throughout the eukaryotic tree of life. Interestingly, MF myosins are nearly always found to play roles in formation of large actin-filament structures including gut microvilli (myosin 7b), stereocilia of the ear (myosin 15), and filopodia of epithelial cells and neurons (myosin 10). This group has shown that Dicty myosin 7 generates filopodia by a mechanism strikingly similar to myosin 10 in humans. The similar functions of MF myosins suggests a shared ancestral function may have been conserved despite extensive gene duplication, a poorly understood aspect of evolution. Another Dicty MF myosin, myosin 44, has an essential role in chemotactic cell migration. In contrast to myosin 7, animals do not possess a homolog to myosin 44 despite common mechanisms of cell migration. Research in this lab uses computational phylogenetic methods to trace the evolution of the MyTH4-FERM myosin gene family. In the case of Dicty myosin 7, ancestral functions appear to have been conserved and diversified during evolution while in the case of myosin 44 it appears that a new function has evolved in the social amoeba. Phylogenetic analysis allows the group to use the MF myosins as a test case for how ancestral functions may be either conserved or lost as new functions emerge in a gene family.

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MSI Users Bulletin – December 2017

The Users Bulletin provides a summary of new policies, procedures, and events of interest to MSI users. It is published quarterly. To request technical assistance with your MSI account, please contact . 1. Annual Account Renewals : The MSI 2017 allocation period ends on December 31...

How can I create private software modules?

Software modules are used to manage the software environment on Linux systems, by allowing users to load and unload particular software versions. Loading a software module sets environmental variables in order to make a particular piece of software accessible. Many pieces of software have been...