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Research has shown that the human microbiome - the community of microorganisms that inhabit our bodies - may have health implications. It’s possible, for example, that a certain mixture of these microorganisms may cause certain diseases.
Researchers have recently begun to study the microbiome in depth. While much recent research has involved the bacteria that live in human bodies, only limited studies have dealt with the fungi that are also present. While there are fewer fungi present in the microbiome than there are bacteria, fungi also affect human health. For example, fungi cause some life-threatening diseases in infants, and other fungi may alleviate intestinal inflammation.
In a recent paper in PLoS One, MSI Principal Investigators Cheryl Gale (Associate Professor of Pediatrics and Genetics, Cell Biology, and Development), Dan Knights (Assistant Professor of Computer Science and Engineering), and Michael Sadowsky (Director, BioTechnology Institute; Professor of Soil, Water, and Climate) describe a new strategy to characterize intestinal fungal communities in infants. The authors used genomic techniques to study and characterize the fungal microbiomes of infants. They also obtained quantitative information about Candida, which is the dominant fungal genus in the human intestine. This work used software available through MSI as well as computational resources. The article can be read on the PLoS One website: Timothy Heisel, Heather Podgorski, Christopher M. Staley, Dan Knights, Michael J. Sadowsky, and Cheryl A. Gale. 2015. Complementary Amplicon-Based Genomic Approaches for the Study of Fungal Communities in Humans. PLoS One 10(2): e0116705. 10.1371/journal.pone.0116705.
Professors Gale, Knights, and Sadowsky use MSI resources to support their research into microbes and the microbiome. Professor Gale is using genomic approaches to establish how intestinal microbiome dynamics are associated with diseases in infants. Professor Knights is helping to create a bioinformatics pipeline for linking genetic variation with bacteria. Professor Sadowsky studies the metagenome of the Mississippi River, soil, and the human intestinal tract.
Image description: Relative Abundances of fungal taxa in infant fecal samples. Sample numbers (each from different infants) are noted on the lower line of the x-axis and the results of triplicate determinations are shown above the sample number for each. The most abundant taxa are indicated on the right-hand side of the graph, with low-abundance (present at <1.5% mean abundance across all samples) being grouped into the “Other” category. Sequencing reads are displayed as percentages of the total number of reads for each individual sequencing replicate. Image and description from Heisel, T, et al., 2015. PLoS One 10(2): e0116705. 10.1371/journal.pone.0116705.
On Thursday, April 23, MSI will hold the sixth annual MSI Research Exhibition and will dedicate our newest supercomputer, Mesabi. Mesabi is an HP distributed cluster featuring a large number of nodes with leading-edge Intel processors that are tightly integrated via a very high speed communication network. In addition, it contains a significant number of nodes with very large memory (up to 1 TB per node), accelerator nodes (GPU), and nodes with solid-state storage devices (SSD) for ultra high performance input/output.
In the Research Exhibition, MSI researchers will present posters of their work using MSI. The posters will be judged by a panel of faculty members and prizes (travel awards) will be awarded. Posters compete in one of two categories, Physical Sciences and Engineering or Biological and Medical Sciences. Entrants are from a wide variety of disciplines. The submitted posters are listed on the MSI website:
Everyone is invited! This is an excellent opportunity to find out about Mesabi and about the research being done among other groups, and to make connections for future collaborations.
The Dedication and Research Exhibition will be held on the fourth and fifth floors of Walter Library. We will also be giving tours of the machine room so that you can see the machine and learn more about its capabilities. Light refreshments will be served. The event page will be updated as details are finalized.
If you’re interested in attending all or part of this occasion, we’d appreciate it if you’d fill in the Google form (linked from the event page linked above) indicating your interest. You don’t have to register to attend, but we want to make sure we order enough refreshments.
Image description: The images were taken from the Grand Prize-winning posters at the 2014 Research Exhibition.
Left: Inferred regulatory network of selected cardiac genes during differentiation. From “Inferring gene regulatory networks in cardiac differentiation by integrating temporal RNA-seq and ChIP-seq data.” Wuming Gong, lead author.
Right: A half-elipsoid mesh was used to model the isolated Pacinian corpuscle (PC). The ellipsoid had a major axis of length 1 mm and a minor axis of length 500 μ-m. Delaunay networks were rotated to become circumferentially aligned within the PC. 10 μm indentation of a cylindrical rod of diameter 250 μm occurred along the +z axis. From “Multiscale mechanical modeling of the Pacinian corpuscle.” Julia Quindlen, lead author.
posted on April 1, 2015
See all Research Spotlights.
Materials whose atoms form a crystal structure - the atoms are organized in a symmetric spatial arrangement - are useful for various applications, such as electronics. During the crystal growth process, dislocations can form. One type is called a “screw dislocation,” which can be seen in the image above. Defects in a crystal will affect its properties and thus have implications for the material’s use.
MSI Principal Investigator Traian Dumitrica, an associate professor in the Department of Mechanical Engineering (College of Science and Engineering), post-doctoral fellow Dr. Yuxiang Ni, and their colleagues at the Ecole Centrale Paris have been studying screw dislocations by performing equilibrium molecular dynamics simulations on MSI’s supercomputers. In a recent paper, these researchers discussed their finding that the area around a screw dislocation in a silicon carbide crystal has higher internal thermal resistance than the rest of the material. This is interesting theoretically, and the findings also can be applied to the design of materials useful for high-temperature electronics and thermoelectric applications. The paper was featured on the cover of the prestigious journal Physical Review Letters in September 2014. (Y Ni, S. Xiong, S. Volz, T. Dumitrica. Thermal transport along the dislocation line in silicon carbide. 2014. Physical Review Letters. 113, 124301).
Professor Dumitrica and his research group use MSI resources for molecular dynamics simulations related to studies of the mechanical properties, stability, and behavior of nanoscale materials. A previous paper was featured in a Research Spotlight, “Modeling Properties of Graphene,” in August 2014.
Image description: Supercells for the SiC calculations: pristine (left), 1b (center) and 2b (right) screw dislocated (b = 3.08 Å). The heat carrying direction is z. The cross-section dimensions are 4 x 4 nm. Length is 7 nm. Image and description Ni, Y et al., PRL, 2014, 113:124301. ©2014 American Physical Society
posted on March 18, 2015
In the fall of 2014, MSI added a Ceph object storage system as an option for second-tier storage for MSI users. Many MSI researchers are in disciplines that use huge amounts of data, such as informatics, genomics, and astrophysics. Often, much of this data does not need to be stored on a machine with high-speed access. This is where a good second-tier storage option is valuable.
The Ceph system currently has 1.4 PB of space for data storage. Its access features allow researchers to exchange data with colleagues outside the University of Minnesota, port cloud-based workflows to MSI systems, and store inactive data separately from the high-performance systems. Several MSI researchers, shown below, have already begun using the Ceph system.
Professor Shaul Hanany (Physics and Astronomy/Minnesota Institute for Astrophysics; College of Science and Engineering) and his research group are analyzing data from the E and B EXperiment (EBEX), a NASA-funded balloon-borne polarimeter designed to measure the polarization of the cosmic microwave background and to develop methods for subtraction of foreground sources from these data. The first science flight of EBEX collected 1 TB of raw data. The Hanany group is performing simulations to understand the uncertainties and systematic effects associated with the data analysis.
Assistant Professor Suzanne McGaugh (Ecology, Evolution, and Behavior; College of Biological Sciences) uses MSI to support genomics and transcriptomics studies in cavefish, reptiles, and other animals. A recent Research Spotlight featured a paper by Professor McGaugh and her colleagues that disclosed the first de novo genome assembly for the cavefish Astyanax mexicanus, the Mexican tetra fish.
Assistant Professor Peter Morrell (Agronomy and Plant Genetics; College of Food, Agricultural, and Natural Resource Sciences) is studying the effect of domestication and strong selection during crop improvement on the level of deleterious mutations in self-fertilizing crops. This involves DNA and RNA sequence assembly, identification of single nucleotide polymorphisms, and using probabilistic approaches to determine the proportion of mutations that are likely to be deleterious.
All these groups have placed terabytes of their data onto the Ceph system. This has freed up space in each group’s allotted quota on the high-performance storage systems, creating a more efficient use of those systems.
posted on March 4, 2015
For centuries, Pacific Islanders have used the kava (Piper methysticum G. Forster) plant to make water-based drinks for medicinal and ceremonial use. Kava, prepared with water, is also traditionally used as a daily drinking beverage at the end a workday similar to a cocktail. Because of reports that linked solvent (e.g. ethanol, acetone) extracted kava use to liver damage, in the early 2000s governments in the European Union, Canada, Australia, and the U.S. have either banned its import or have issued consumer advisories. In spite of this, kava use as an alternative medicine continues, and export data show that consumption is even increasing. Some earlier studies have indicated that kava may have some properties as a cancer preventative. However, not only are there different classes and varieties of kava cultivars, differences in the preparation of kava drinks results in considerable variations in the amount of compounds in the drinks.
Two MSI Principal Investigators, Associate Professor Adrian D. Hegeman (Horticultural Science; College of Food, Agricultural, and Natural Resource Sciences) and Professor Chengguo Xing (Medicinal Chemistry; College of Pharmacy), are authors on a recent paper in PLoS One that measured variations in cellular toxicity (cytotoxicity) and chemical composition in several different commercially available kava products. The lead author, Amanda C. Martin, recently graduated from Professor Hegeman’s MSI research group. The researchers used metabolomics to study the compounds in kava and to assess their potential as cancer preventatives. They also studied six compounds that may be associated with medicinal or negative cytotoxic effects of kava. Results showed that not only is there wide variability in chemical composition and cytotoxicity among commercial kava drinks, the possible benefits of kava as a cancer preventative indicate that it should be studied further. The paper can be found on the PLoS One website. (Amanda C. Martin, Ed Johnston, Chengguo Xing, and Adrian D. Hegeman. 2014. Measuring the chemical and cytotoxic variability of commercially available kava (Piper methysticum G. Forster). PloS One 9, (11) (NOV 03), 10.1371/journal.pone.0111572.)
Image description: Left: Comparison of relative cell viability to flavokawain (FLK) A and B concentrations. Top: Relative cell viability of human lung adenocarcinoma A549 cancer cell line after 48-hour incubation with kava extracts in ethanol solvent at 75 mg/mL. Samples are organized from coarse grind on the left to very fine grind on the right with the last three dry powder samples (P, Z, and V) being instant freeze-dried kava. Black bars represent liquid samples. Bottom: Concentration of two potentially cytotoxic compounds found in kava (white bars: FLKA and black bars: FLKB). Error bars represent standard error of 3-4 replicates. Image and description are from Martin, AC, et al., PloS One 9(11), 10.1371/journal.pone.0111572. Right: The Hawaiian ‘awa cultivar ‘Awa Papa ‘Ele’ele (photo courtesy Ed Johnson).
posted on February 18, 2015