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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
Concern about the level of greenhouse gases in the atmosphere and the resulting impacts on global climate has led many to look for alternative technologies. Since automobiles have become a major source of greenhouse gases, scientists and engineers have been working to develop cars that run on alternative fuels. There are a number of options, including using fuels other than gasoline in internal-combustion engines and using electric or hybrid-electric vehicles. However, whether a given alternative fuel actually has less impact than gasoline can be unclear.
Christopher Tessum, a graduate student in the research group of Associate Professor Julian Marshall (Fellow, Institute on the Environment; Civil, Environmental, and Geo- Engineering, College of Science and Engineering), is the lead author on a recent paper that uses computer modeling to investigate impact on air quality of several kinds of alternative fuels. The researchers are also able to predict the resulting health impacts from changes in air quality. Assistant Professor Jason Hill (Bioproducts and Biosystems Engineering, College of Science and Engineering and College of Food, Agricultural, and National Resource Sciences) and Professor Marshall are corresponding authors on the paper, which appeared in the Proceedings of the National Academy of Science of the United States of America in December 2014 (Tessum, Christopher W., Jason D. Hill, and Julian D. Marshall. 2014. Life cycle air quality impacts of conventional and alternative light-duty transportation in the United States. Proceedings of the National Academy of Sciences of the United States of America 111(52) (DEC 30), 10.1073/pnas.1406853111.). The simulations estimated two pollutants, fine particulate matter and ground-level ozone, and used population and epidemiological data to estimate mortality from various scenarios.
One of the features of this paper is that it not only studies the impact of emissions from the vehicles themselves, but it includes data about emissions from the source of the fuel - for example, the emissions from coal burned at the electric power plant that provided the electricity for a hybrid vehicle. The researchers found that electric vehicles that are powered by electricity generated from natural gas or wind, water, or solar power are best for air quality. Videos that describe the research and show the simulations of particulate matter and ozone are available on the Marshall group’s website.
Articles about this paper have appeared in various media outlets:
- Popular Mechanics
- The Economist
- Pioneer Press (St. Paul, Minnesota)
- University of Minnesota Discover blog
The Marshall research group at MSI has numerous publications concerning their research into the health effects of air quality issues. A previous Research Spotlight (Air Pollution and Socioeconomic Status, September 17, 2014) featured a paper that appeared in PLoS One in April 2014.
Image description: Annual average particulate matter concentrations. (A) Year 2005 baseline modeled concentrations. (B-L) Increase in concentration above the baseline attributable to replacement of 10% of year 2020 vehicle use with the given technology. (M) Increase in concentration attributable to EV battery manufacturing. Color scales contain a discontinuity at the 99th percentile of emissions. Abbreviations: CNG, compressed natural gas vehicle; EV, electric vehicle; WWS, wind, water, or solar. Image and description, Tessum CW et al., PNAS 2014;111:18490018495. ©National Academy of Sciences of the United States of America.
posted on February 4, 2015
Plasmas are used in industrial processes in several important high-technology industries, such as the semiconductor industry. One application is the use of chemically reactive plasmas to deposit extremely thin films on other materials. So-called “dusty” plasmas contain particulates; these plasmas are of great interest to industry, as particulates can be a source of contamination during the manufacturing processes, especially when the particulates are in the nano scale.
The behavior of these dusty plasmas has been studied by researchers in the group of Regents Professor Donald Truhlar (Chemistry; MSI Fellow). The Truhlar group is involved in a wide-ranging research program that is in the forefront of computational chemistry, including the structure and reactivity of nanoparticles. The research uses quantum mechanical, and quantum statistical methods. Much of this work is done using codes that have been developed by the Truhlar group themselves; they also use commercially available codes.
In a recent publication in the Journal of the American Chemical Society, post-doctoral researcher Dr. Prasenjit Seal and Professor Truhlar studied the thermodynamic properties of silane plasmas, which are widely used to grow silicon materials of use in electronics, photovoltaics, and photonics (Seal, Prasenjit and Donald Truhlar. 2014. Large entropic effects on the thermochemistry of silicon nanodusty plasma constituents. Journal of the American Chemical Society 136 (7): 2786-99). This research used a statistical mechanical approach combined with density functional theory. The authors studied five categories of silicon hydride clusters and radicals, including silanes, silyl radicals, and silenes, and showed the importance of multistructural effects.
The Truhlar group publishes a large number of papers every year and collaborates with many faculty researchers at the University of Minnesota and elsewhere. Some MSI Principal Investigators collaborating with Professor Truhlar include chemistry Professors Chris Cramer, Laura Gagliardi, and Jiali Gao, and medicinal chemistry Associate Professor Elizabeth Amin. Professor Truhlar is also a member of the Chemical Theory Center.
Other recent publications by the Truhlar group include:
- Klippenstein, Stephen J., Vijay S. Pande, and Donald G. Truhlar. 2014. Chemical kinetics and mechanisms of complex systems: A perspective on recent theoretical advances. Journal of the American Chemical Society 136 (2) (JAN 15): 528-46.
- Lee, Kyuho, William C. Isley, III, Allison L. Dzubak, Pragya Verma, Samuel J. Stoneburner, Li-Chiang Lin, Joshua D. Howe, et al. [Christopher Cramer; Donald Truhlar; Laura Gagliardi] 2014. Design of a metal-organic framework with enhanced back bonding for separation of N-2 and CH4. Journal of the American Chemical Society 136 (2) (JAN 15): 698-704.
- Xu, Xuefei, Jingjing Zheng, Ke R. Yang, and Donald G. Truhlar. 2014. Photodissociation dynamics of phenol: Multistate trajectory simulations including tunneling. Journal of the American Chemical Society 136 (46) (NOV 19): 16378-86.
- Zheng, Jingjing, Ruben Meana-Paneda, and Donald G. Truhlar. 2014. Prediction of experimentally unavailable product branching ratios for biofuel combustion: The role of anharmonicity in the reaction of isobutanol with OH. Journal of the American Chemical Society 136 (13) (APR 2): 5150-60.
- Han, Jaebeom, Michael J. M. Mazack, Peng Zhang, Donald G. Truhlar, and Jiali Gao. 2013. Quantum mechanical force field for water with explicit electronic polarization. Journal of Chemical Physics 139 (5) (AUG 7): 054503.
- Ho, Junming, Jingjing Zheng, Ruben Meana-Paneda, Donald G. Truhlar, Eun Jung Ko, G. Paul Savage, Craig M. Williams, Michelle L. Coote, and John Tsanaktsidis. 2013. Chloroform as a hydrogen atom donor in Barton reductive decarboxylation reactions. Journal of Organic Chemistry 78 (13) (JUL 5): 6677-87.
- Jalan, Amrit, Ionut M. Alecu, Ruben Meana-Paneda, Jorge Aguilera-Iparraguirre, Ke R. Yang, Shamel S. Merchant, Donald G. Truhlar, and William H. Green. 2013. New pathways for formation of acids and carbonyl products in low-temperature oxidation: The Korcek decomposition of gamma-ketohydroperoxides. Journal of the American Chemical Society 135 (30) (JUL 31): 11100-14.
- Kurbanov, Elbek K., Hannah R. Leverentz, Donald G. Truhlar, and Elizabeth A. Amin. 2013. Analysis of the errors in the electrostatically embedded many-body expansion of the energy and the correlation energy for Zn and Cd coordination complexes with five and six ligands and use of the analysis to develop a generally successful fragmentation strategy. Journal of Chemical Theory and Computation 9 (6) (JUN): 2617-28.
- Marenich, Aleksandr V., Christopher J. Cramer, and Donald G. Truhlar. 2013. Uniform treatment of solute-solvent dispersion in the ground and excited electronic states of the solute based on a solvation model with state-specific polarizability. Journal of Chemical Theory and Computation 9 (8) (AUG): 3649-59.
- Maurice, Remi, Pragya Verma, Joseph M. Zadrozny, Sijie Luo, Joshua Borycz, Jeffrey R. Long, Donald G. Truhlar, and Laura Gagliardi. 2013. Single-ion magnetic anisotropy and isotropic magnetic couplings in the metal-organic framework Fe-2(dobdc). Inorganic Chemistry 52 (16) (AUG 19): 9379-89.
Image description: M06-L/MG3S optimized global-minimum-energy structures of the largest representatives for each of the classes of systems considered in the paper: (a) fully branched silanes, Si10H22-FB; (b) unbranched silanes, n-Si9H20; (c) fully branched silyl radicals, Si7H15-FB; (d) unbranched silyl radicals, types I, II, and III, Si6H13; (e) fully branched silenes, Si6H12-FB; and (f) iso-Si7H16. Si atoms are black, and H atoms are light gray. (P. Seal and D. Truhlar, JACS 136(7):2786 (2014) © American Chemical Society)
posted on January 21, 2015
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Sirtuins are a group of seven compounds (SIRT1 - SIRT7) that are involved in a wide range of biological functions. Because of their role in gene regulation, researchers believe that sirtuin inhibitors may be useful as treatments for diseases. For example, drug designers believe that SIRT2 inhibition could be a useful treatment for Parkinson’s disease.
MSI Principal Investigator Liqiang Chen, an assistant professor in the Center for Drug Design in the Academic Health Center, and his colleagues recently published a paper discussing a method of creating SIRT2 inhibitors. The method uses fragments of other compounds that have characteristics that would be useful in the compound. The researchers combine the fragments in new ways, and then analyze their activity. One of these new compounds, dubbed “compound 64” by the researchers, showed particular promise as a SIRT2 inhibitor. It was also notable in that it was very selective in interacting with SIRT2 but not with its most similar sirtuins, SIRT1 or SIRT3.
Once the researchers had identified compound 64 as a likely candidate for further research, they used MSI resources to perform computational modeling to study how it attaches to SIRT2. While this research is preliminary, compound 64 shows promise as a possible treatment for the symptoms of Parkinson’s disease. Professor Chen and his colleagues are continuing their investigations into compound 64.
This research has been supported by the Center for Drug Design at the University of Minnesota. The group’s paper can be found on the Journal of Medicinal Chemistry website: Cui, Huaqing, Zeeshan Kamal, Teng Ai, Yanli Xu, Swati S. More, Daniel J. Wilson, and Liqiang Chen. 2014. Discovery of Potent and Selective Sirtuin 2 (SIRT2) Inhibitors Using a Fragment-Based Approach. Journal of Medicinal Chemistry 57 (20): 8340-57.
Image description: Potential binding modes and interactions of compound 64 docked into the crystal structure of SIRT2 (PDB entry 1j8f). (A) Two binding modes of compound 64 in the active site of SIRT2 (surface representation). (B) Potental interactions between compound 64 and SIRT2 in the first binding mode (magenta). (C) Potential interactions between compound 64 and SIRT2 in the second mode (green). Image and description, Cui, H. et al., J Med Chem 57 (20): 8340-57 (2014). ©2014 American Chemical Society.
posted on January 7, 2015