WorldWideScience

Sample records for riken omics science

  1. RIKEN accelerator progress report, vol. 36. January - December 2002

    International Nuclear Information System (INIS)

    Asahi, K.; Abe, T.; Ichihara, T.

    2003-03-01

    This issue of RIKEN Accelerator Progress Report reports research activities of the RIKEN Accelerator Research Facility (RARF) during the calendar year of 2002. The research programs have been coordinated in the framework of the project entitled Multidisciplinary Researches on Heavy Ion Science. The project involves a variety of fields such as: nuclear physics, nuclear astrophysics, atomic physics, nuclear chemistry, radiation biology, condensed matter physics in terms of accelerator or radiation application, plant mutation, material characterization, application to space science, accelerator physics and engineering, laser technology, and computational technology. These activities involved ten laboratories, five Centers involving seven divisions, the RIKEN-RAL (Rutherford-Appleton Laboratory) Center, and the RBRC (RIKEN-Brookhaven Research Center at Brookhaven National Laboratory), and more than 350 researchers from domestic and foreign institutions. Thirty-six universities and institutes from within Japan and 33 institutes from 10 countries are involved. (J.P.N.)

  2. RIKEN radioactive isotope beam factory project – Present status and ...

    Indian Academy of Sciences (India)

    Programs for studying nuclear reactions and structure of exotic nuclei available at the RIKEN radioactive isotope beam factory project are introduced and discussed by demonstrating recent highlights. Special emphasis ... RIKEN Nishina Center for Accelerator-Based Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan ...

  3. The state of rhizospheric science in the era of multi-omics: A practical guide to omics technologies

    Energy Technology Data Exchange (ETDEWEB)

    White, Richard Allen; Rivas-Ubach, Albert; Borkum, Mark I.; Köberl, Martina; Bilbao, Aivett; Colby, Sean M.; Hoyt, David W.; Bingol, Kerem; Kim, Young-Mo; Wendler, Jason P.; Hixson, Kim K.; Jansson, Christer

    2017-06-01

    Over the past century, the significance of the rhizosphere as a complex, biological system, comprised of vast, interconnected networks of microbial organisms that interact directly with their plant hosts (e.g., archæa, bacteria, fungi, eukaryotes, and viruses) has been increasingly recognized by the scientific community. Providing a nutritional base to the terrestrial biosphere, the rhizosphere is integral to plant growth, crop production and ecosystem health. Lack of mechanistic understanding of the rhizosphere constitutes a critical knowledge gap, inhibiting our ability to predict and control the terrestrial ecosystem in order to achieve desirable outcomes (e.g., bioenergy production, crop yield maximization, and soilbased carbon sequestration). Application of multi-omics has the potential to significantly advance our knowledge of rhizospheric science. This review covers: cutting- and bleeding-edge, multi-omic techniques and technologies; methods and protocols for specific rhizospheric science questions; and, challenges to be addressed during this century of rhizospheric science.

  4. Proceedings of RIKEN BNL Research Center Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Samios, Nicholas P. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2013-01-24

    The twelfth evaluation of the RIKEN BNL Research Center (RBRC) took place on November 6 – 8, 2012 at Brookhaven National Laboratory. The members of the Scientific Review Committee (SRC), present at the meeting, were: Prof. Wit Busza, Prof. Miklos Gyulassy, Prof. Kenichi Imai, Prof. Richard Milner (Chair), Prof. Alfred Mueller, Prof. Charles Young Prescott, and Prof. Akira Ukawa. We are pleased that Dr. Hideto En’yo, the Director of the Nishina Institute of RIKEN, Japan, participated in this meeting both in informing the committee of the activities of the RIKEN Nishina Center for Accelerator- Based Science and the role of RBRC and as an observer of this review. In order to illustrate the breadth and scope of the RBRC program, each member of the Center made a presentation on his/her research efforts. This encompassed three major areas of investigation: theoretical, experimental and computational physics. In addition, the committee met privately with the fellows and postdocs to ascertain their opinions and concerns. Although the main purpose of this review is a report to RIKEN management on the health, scientific value, management and future prospects of the Center, the RBRC management felt that a compendium of the scientific presentations are of sufficient quality and interest that they warrant a wider distribution. Therefore we have made this compilation and present it to the community for its information and enlightenment.

  5. Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science).

    Science.gov (United States)

    Zeng, Irene Sui Lan; Lumley, Thomas

    2018-01-01

    Integrated omics is becoming a new channel for investigating the complex molecular system in modern biological science and sets a foundation for systematic learning for precision medicine. The statistical/machine learning methods that have emerged in the past decade for integrated omics are not only innovative but also multidisciplinary with integrated knowledge in biology, medicine, statistics, machine learning, and artificial intelligence. Here, we review the nontrivial classes of learning methods from the statistical aspects and streamline these learning methods within the statistical learning framework. The intriguing findings from the review are that the methods used are generalizable to other disciplines with complex systematic structure, and the integrated omics is part of an integrated information science which has collated and integrated different types of information for inferences and decision making. We review the statistical learning methods of exploratory and supervised learning from 42 publications. We also discuss the strengths and limitations of the extended principal component analysis, cluster analysis, network analysis, and regression methods. Statistical techniques such as penalization for sparsity induction when there are fewer observations than the number of features and using Bayesian approach when there are prior knowledge to be integrated are also included in the commentary. For the completeness of the review, a table of currently available software and packages from 23 publications for omics are summarized in the appendix.

  6. A flexible representation of omic knowledge for thorough analysis of microarray data

    Directory of Open Access Journals (Sweden)

    Demura Taku

    2006-03-01

    used for microarray data analysis with GSCope3. In addition to BiKLi, by collecting various types of omic knowledge as OSML libraries, it becomes possible for us to conduct detailed thorough analysis from various biological viewpoints. GSCope3 and BiKLi are available for academic users at our web site http://omicspace.riken.jp.

  7. ECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach.

    Directory of Open Access Journals (Sweden)

    Yoshiyuki Ogata

    Full Text Available Ecosystems can be conceptually thought of as interconnected environmental and metabolic systems, in which small molecules to macro-molecules interact through diverse networks. State-of-the-art technologies in post-genomic science offer ways to inspect and analyze this biomolecular web using omics-based approaches. Exploring useful genes and enzymes, as well as biomass resources responsible for anabolism and catabolism within ecosystems will contribute to a better understanding of environmental functions and their application to biotechnology. Here we present ECOMICS, a suite of web-based tools for ECosystem trans-OMICS investigation that target metagenomic, metatranscriptomic, and meta-metabolomic systems, including biomacromolecular mixtures derived from biomass. ECOMICS is made of four integrated webtools. E-class allows for the sequence-based taxonomic classification of eukaryotic and prokaryotic ribosomal data and the functional classification of selected enzymes. FT2B allows for the digital processing of NMR spectra for downstream metabolic or chemical phenotyping. Bm-Char allows for statistical assignment of specific compounds found in lignocellulose-based biomass, and HetMap is a data matrix generator and correlation calculator that can be applied to trans-omics datasets as analyzed by these and other web tools. This web suite is unique in that it allows for the monitoring of biomass metabolism in a particular environment, i.e., from macromolecular complexes (FT2DB and Bm-Char to microbial composition and degradation (E-class, and makes possible the understanding of relationships between molecular and microbial elements (HetMap. This website is available to the public domain at: https://database.riken.jp/ecomics/.

  8. Meeting report: Ocean 'omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013).

    Science.gov (United States)

    Gilbert, Jack A; Dick, Gregory J; Jenkins, Bethany; Heidelberg, John; Allen, Eric; Mackey, Katherine R M; DeLong, Edward F

    2014-06-15

    The National Science Foundation's EarthCube End User Workshop was held at USC Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterize the needs and tools available to the community that is focusing on microbial and physical oceanography research with a particular emphasis on 'omic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analyzing the existing data, on the need for the construction and curation of diverse federated databases, as well as development of shared, interoperable, "big-data capable" analytical tools. The key outputs from this workshop include (i) critical scientific challenges and cyber infrastructure constraints, (ii) the current and future ocean 'omics science grand challenges and questions, and (iii) data management, analytical and associated and cyber-infrastructure capabilities required to meet critical current and future scientific challenges. The main thrust of the meeting and the outcome of this report is a definition of the 'omics tools, technologies and infrastructures that facilitate continued advance in ocean science biology, marine biogeochemistry, and biological oceanography.

  9. Omics Research on the International Space Station

    Science.gov (United States)

    Love, John

    2015-01-01

    The International Space Station (ISS) is an orbiting laboratory whose goals include advancing science and technology research. Completion of ISS assembly ushered a new era focused on utilization, encompassing multiple disciplines such as Biology and Biotechnology, Physical Sciences, Technology Development and Demonstration, Human Research, Earth and Space Sciences, and Educational Activities. The research complement planned for upcoming ISS Expeditions 45&46 includes several investigations in the new field of omics, which aims to collectively characterize sets of biomolecules (e.g., genomic, epigenomic, transcriptomic, proteomic, and metabolomic products) that translate into organismic structure and function. For example, Multi-Omics is a JAXA investigation that analyzes human microbial metabolic cross-talk in the space ecosystem by evaluating data from immune dysregulation biomarkers, metabolic profiles, and microbiota composition. The NASA OsteoOmics investigation studies gravitational regulation of osteoblast genomics and metabolism. Tissue Regeneration uses pan-omics approaches with cells cultured in bioreactors to characterize factors involved in mammalian bone tissue regeneration in microgravity. Rodent Research-3 includes an experiment that implements pan-omics to evaluate therapeutically significant molecular circuits, markers, and biomaterials associated with microgravity wound healing and tissue regeneration in bone defective rodents. The JAXA Mouse Epigenetics investigation examines molecular alterations in organ specific gene expression patterns and epigenetic modifications, and analyzes murine germ cell development during long term spaceflight. Lastly, Twins Study ("Differential effects of homozygous twin astronauts associated with differences in exposure to spaceflight factors"), NASA's first foray into human omics research, applies integrated analyses to assess biomolecular responses to physical, physiological, and environmental stressors associated

  10. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP: VOLUME 61 RIKEN-TODAI MINI-WORKSHOP ON ''TOPICS IN HADRON PHYSICS AT RHIC''. VOLUME 61

    International Nuclear Information System (INIS)

    EN'YO, H.; HAMAGAKI, H.; HATSUDAT WATANABA, Y.; YAZAKI, K.

    2004-01-01

    The RIKEN-TODAI Mini-Workshop on ''Topics in Hadron Physics at RHIC'' was held on March 23rd and 24th, 2064 at the Nishina Memorial Hall of RIKEN, Wako, Saitama, Japan, sponsored by RIKEN (Institute of Physical and Chemical Research) and TODAI (University of Tokyo). The workshop was planned when we learned that two distinguished theorists in hadron physics, Professors L. McLerran and S.H. Lee, would be visiting TODAI and/or RIKEN during the week of March 22-26. We asked them to give key talks at the beginning of the workshop and attend the sessions consisting of talks by young theorists in RIKEN, TODAI and other institutes in Japan and they kindly agreed on both. Considering the JPS meeting scheduled from March 27 through 30, we decided to have a.one-and-half-a-day workshop on March 23 and 24. The purpose of the workshop was to offer young researchers an opportunity to learn the forefront of hadron physics as well as to discuss their own works with the distinguished theorists

  11. OMICs technologies: tools for food science

    National Research Council Canada - National Science Library

    Benkeblia, Noureddine

    2012-01-01

    ... in the transformation from industrial to sustained food technologies and the role of these omics tools to mitigate the growing pressure of limited natural resources and environmental degradation...

  12. Recent radioactive ion beam program at RIKEN and related topics

    Indian Academy of Sciences (India)

    Keywords. RIKEN; radioactive ion beams; magic numbers. PACS No. 21.10.-k. 1. Introduction. In RIKEN, there are several heavy ion accelerators. Main accelerator is the RIKEN ring cyclotron (RRC) with K = 540, that has been operated from 1986. The RRC has two injectors; one is heavy ion linear accelerator that has been ...

  13. Meeting report: Ocean ‘omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013)

    Science.gov (United States)

    Gilbert, Jack A; Dick, Gregory J.; Jenkins, Bethany; Heidelberg, John; Allen, Eric; Mackey, Katherine R. M.

    2014-01-01

    The National Science Foundation’s EarthCube End User Workshop was held at USC Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterize the needs and tools available to the community that is focusing on microbial and physical oceanography research with a particular emphasis on ‘omic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analyzing the existing data, on the need for the construction and curation of diverse federated databases, as well as development of shared, interoperable, “big-data capable” analytical tools. The key outputs from this workshop include (i) critical scientific challenges and cyber infrastructure constraints, (ii) the current and future ocean ‘omics science grand challenges and questions, and (iii) data management, analytical and associated and cyber-infrastructure capabilities required to meet critical current and future scientific challenges. The main thrust of the meeting and the outcome of this report is a definition of the ‘omics tools, technologies and infrastructures that facilitate continued advance in ocean science biology, marine biogeochemistry, and biological oceanography. PMID:25197495

  14. Physics of the 1 Teraflop RIKEN-BNL-Columbia QCD project. Proceedings of RIKEN BNL Research Center workshop: Volume 13

    International Nuclear Information System (INIS)

    1998-01-01

    A workshop was held at the RIKEN-BNL Research Center on October 16, 1998, as part of the first anniversary celebration for the center. This meeting brought together the physicists from RIKEN-BNL, BNL and Columbia who are using the QCDSP (Quantum Chromodynamics on Digital Signal Processors) computer at the RIKEN-BNL Research Center for studies of QCD. Many of the talks in the workshop were devoted to domain wall fermions, a discretization of the continuum description of fermions which preserves the global symmetries of the continuum, even at finite lattice spacing. This formulation has been the subject of analytic investigation for some time and has reached the stage where large-scale simulations in QCD seem very promising. With the computational power available from the QCDSP computers, scientists are looking forward to an exciting time for numerical simulations of QCD

  15. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER, RIKEN WINTER SCHOOL, QUARK GLUON STRUCTURE OF THE NUCLEON AND QCD, MARCH 29-31, 2002.

    Energy Technology Data Exchange (ETDEWEB)

    EN YO,H.; SAITO,N.; SHIBATA,T.A.; YAZAKI,K.; BUNCE,G.

    2002-03-29

    The RIKEN School on ''Quark-Gluon Structure of the Nucleon and QCD'' was held from March 29th through 31st at the Nishina Memorial Hall of RIKEN, Wako, Saitama, Japan, sponsored by RIKEN (the Institute of Physical and Chemical Research). The school was the second of a new series with a broad perspective of hadron and nuclear physics. The purpose of the school was to offer young researchers an opportunity to learn theoretical aspects of hadron physics based on QCD and related experimental programs being or to be carried out by Japanese groups. We had 3 theoretical courses, each consisting of 3 one-hour lectures, and 6 experimental courses, each consisting of a one-hour lecture.

  16. Trichromatic concept at the SPring-8 RIKEN beamline I

    International Nuclear Information System (INIS)

    Yamamoto, Masaki; Kumasaka, Takashi; Ueki, Tatzuo

    1998-01-01

    At the SPring-8, RIKEN beamline I has been designed and developed for structural biology research by the Institute of Physical and Chemical Research (RIKEN). RIKEN beamline I consists of two experimental stations, protein crystallography (PX) and small-angle X-ray scattering (SAXS). Both experiments can be carried out simultaneously, with dichromatic synchrotron radiation emitted from two coaxial undulators with vertical polarization. The branched beams are generated by a transparent diamond crystal. With synchrotron radiation, the multi-wavelength anomalous diffraction (MAD) method, which gives phases from a single anomalous scatterer, has been developed. Anomalous scattering contributes a small portion of diffraction intensity so that the accuracy of intensity data is definitely important. The PX branch of RIKEN beamline I has been designed based on a 'trichromatic concept' to optimize for the MAD data collection. This concept is that three kinds of intensity data sets with three different wavelengths are taken quasi-simultaneously for the single protein crystal without changing any setting by 'trichromator'. The main feature of this concept is to minimize systematic errors in the measurements of anomalous diffraction for the MAD method. The construction of RIKEN beamline I had been progressed satisfactorily until June 1997. The initial commissioning successfully provided the three different monochromatized undulator beams were successfully observed on the phosphor screen, which located at the near end of the trichromator. (author)

  17. Recent radioactive ion beam program at RIKEN and related topics

    Indian Academy of Sciences (India)

    Recent experimental programs at RIKEN concerning RI beams are reviewed. RIKEN has the ring cyclotron (RRC) with high intense heavy-ion beams and large acceptance fragment separator, RIPS. The complex can provide high intense RI-beams. By using the high intense RI-beams, a variety of experiments have been ...

  18. Radio frequency system of the RIKEN ring cyclotron

    International Nuclear Information System (INIS)

    Fujisawa, T.; Ogiwara, K.; Kohara, S.; Oikawa, Y.; Yokoyama, I.; Nagase, M.; Takeshita, I.; Chiba, Y.; Kumata, Y.

    1987-01-01

    The radio-frequency(RF) system of the RIKEN ring cyclotron(K = 540) is required to work in a frequency range of 20 to 45 MHz and to generate the maximum acceleration voltage 250 kV. A new movable box type variable frequency resonator was designed for that purpose. The final amplifier is capable to deliver 300 kW. The resonators and the amplifiers have been installed at RIKEN and the performances are studied. The result shows the movable box type resonator and the power amplifier system satisfy the design aim. (author)

  19. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP CIRCUM-PAN-PACIFIC RIKEN SYMPOSIUM ON HIGH ENERGY SPIN PHYSICS, VOLUME 25

    Energy Technology Data Exchange (ETDEWEB)

    KUMANO,S.; SHIBATA,T.A.; YAZAKI,K.

    2000-06-28

    The Circum-Pan-Pacific Riken Symposium on High Energy Spin Physics was held at Oukouchi Memorial Hall in Riken from November 3 through 6, 1999. It was held as a joint meeting of the 2nd Circum-Pan-Pacific Symposium on High Energy Spin Physics and the 3rd of the series of Riken Symposia related to the RHIC-SPIN. The 1st Circum-Pan-Pacific Symposium on High Energy Spin Physics was held at Kobe in 1996 and the RHIC-SPIN Riken Symposia had been held every two years since 1995. As Prof. Ozaki mentioned in his talk at the beginning of this meeting, the RHIC was ready for the first beam, physics experiments scheduled in 2000, and the RHIC-SPIN would start in 2001. It was therefore considered to be very timely for the researchers in the field of high energy spin physics to get together, clarifying the present status of the field and discussing interesting and important topics as well as experimental subjects to be pursued. It is especially important for the success of the RHIC-SPIN project that the researchers in the neighboring countries surrounding the Pacific are actively involved in it. This is why the above two series were joined in this. symposium. The subjects discussed in the symposium include: Hard processes probing spin-structure functions, polarization mechanisms in high energy reactions, lattice studies of polarized structure functions, theoretical models for the nucleon and its spin structure, RHIC and RHIC-SPIN projects, results and future projects of existing experimental facilities. Totally 73 scientists participated in the symposium, 27 from abroad and 46 from Japan. it consisted of 13 main sessions, with 33 invited and contributed talks, and 4 discussion sessions covering recent experimental and theoretical developments and important topics in high energy spin physics and closely related fields.

  20. RIKEN SCHOOL ON QCD TOPICS ON THE PROTON

    International Nuclear Information System (INIS)

    ENYO, H.; HAYAKAWA, M.; KAWAI, H.; SAITO, N.; SHIBATA, T.A.; TADA, T.; WATANABE, Y.; YAZAKI, K.

    2003-01-01

    The RIKEN School on QCD titled ''Topics on the Proton'' was held on March 26th, 2003 at the Nishina Memorial Hall of RIKEN, Wako, Saitama, Japan, sponsored by REEN (the Institute of Physical and Chemical Research). The school was the third of a new series with a broad perspective of hadron and nuclear physics. The organization and the size of the school were a little different from those of the previous ones. Prof. John Ellis, known as the world best theorist in particle and nuclear physics, has been appointed in RIKEN as an Eminent Scientist, which enables us to plan a collaboration with him for coming three years. As the first year activity, we asked him to give a keynote talk in the JPS spring meeting focusing on the structure of proton, and also to give lectures in RIKEN for younger Japanese scientists on the subjects related the structure of the proton. He kindly agreed on both and we then decided to have a one-day school by supplementing his course with a course on experimental aspects of the proton structure. One of us (N.S.) agreed to give the latter. This time, Theoretical Physics Laboratory joined Radiation Laboratory to organize the school. The purpose of the school was to offer young researchers an opportunity to learn theoretical aspects of the proton structure with a broad perspective including supersymmetry and the related experimental aspects. We had a theoretical course consisting of 3 one-hour lectures by Prof. Ellis and a experimental course consisting of 2 one-hour lectures by Prof. Saito

  1. RIKEN SCHOOL ON QCD TOPICS ON THE PROTON.

    Energy Technology Data Exchange (ETDEWEB)

    En' yo, H.; Kawai, H.; Saito, N.; Shibata, T. A.; Tada, T.; Watanabe, Y.; Yazaki, K.

    2003-10-01

    The RIKEN School on QCD titled ''Topics on the Proton'' was held on March 26th, 2003 at the Nishina Memorial Hall of RIKEN, Wako, Saitama, Japan, sponsored by REEN (the Institute of Physical and Chemical Research). The school was the third of a new series with a broad perspective of hadron and nuclear physics. The organization and the size of the school were a little different from those of the previous ones. Prof. John Ellis, known as the world best theorist in particle and nuclear physics, has been appointed in RIKEN as an Eminent Scientist, which enables us to plan a collaboration with him for coming three years. As the first year activity, we asked him to give a keynote talk in the JPS spring meeting focusing on the structure of proton, and also to give lectures in RIKEN for younger Japanese scientists on the subjects related the structure of the proton. He kindly agreed on both and we then decided to have a one-day school by supplementing his course with a course on experimental aspects of the proton structure. One of us (N.S.) agreed to give the latter. This time, Theoretical Physics Laboratory joined Radiation Laboratory to organize the school. The purpose of the school was to offer young researchers an opportunity to learn theoretical aspects of the proton structure with a broad perspective including supersymmetry and the related experimental aspects. We had a theoretical course consisting of 3 one-hour lectures by Prof. Ellis and a experimental course consisting of 2 one-hour lectures by Prof. Saito.

  2. From data to knowledge: The future of multi-omics data analysis for the rhizosphere

    Energy Technology Data Exchange (ETDEWEB)

    Allen White, Richard; Borkum, Mark I.; Rivas-Ubach, Albert; Bilbao, Aivett; Wendler, Jason P.; Colby, Sean M.; Köberl, Martina; Jansson, Christer

    2017-06-01

    The rhizosphere is the interface between a plant's roots and its surrounding soil. The rhizosphere microbiome, a complex microbial ecosystem, nourishes the terrestrial biosphere. Integrated multi-omics is a modern approach to systems biology that analyzes and interprets the datasets of multiple -omes of both individual organisms and multi-organism communities and consortia. The successful usage and application of integrated multi-omics to rhizospheric science is predicated upon the availability of rhizosphere-specific data, metadata and software. This review analyzes the availability of multi-omics data, metadata and software for rhizospheric science, identifying potential issues, challenges and opportunities.

  3. Proceedings of RIKEN BNL Research Center Workshop: Thermal Photons and Dileptons in Heavy-Ion Collisions. Volume 119

    Energy Technology Data Exchange (ETDEWEB)

    David, G. [Brookhaven National Laboratory (BNL), Upton, NY (United States); Rapp, R. [Brookhaven National Laboratory (BNL), Upton, NY (United States); Ruan, L. [Brookhaven National Laboratory (BNL), Upton, NY (United States); Yee, H-U. [Brookhaven National Laboratory (BNL), Upton, NY (United States)

    2014-09-11

    The RIKEN BNL Research Center (RBRC) was established in April 1997 at Brookhaven National Laboratory. It is funded by the ''Rikagaku Kenkyusho'' (RIKEN, The Institute of Physical and Chemical Research) of Japan and the U. S. Department of Energy’s Office of Science. The RBRC is dedicated to the study of strong interactions, including spin physics, lattice QCD, and RHIC physics through the nurturing of a new generation of young physicists. The RBRC has theory, lattice gauge computing and experimental components. It is presently exploring the possibility of an astrophysics component being added to the program. The primary theme for this workshop related to sharing the latest experimental and theoretical developments in area of low transverse momentum (pT) dielectron and photons. All the presentations given at the workshop are included in this proceedings, primarily as PowerPoint presentations.

  4. Data mining in newt-omics, the repository for omics data from the newt.

    Science.gov (United States)

    Looso, Mario; Braun, Thomas

    2015-01-01

    Salamanders are an excellent model organism to study regenerative processes due to their unique ability to regenerate lost appendages or organs. Straightforward bioinformatics tools to analyze and take advantage of the growing number of "omics" studies performed in salamanders were lacking so far. To overcome this limitation, we have generated a comprehensive data repository for the red-spotted newt Notophthalmus viridescens, named newt-omics, merging omics style datasets on the transcriptome and proteome level including expression values and annotations. The resource is freely available via a user-friendly Web-based graphical user interface ( http://newt-omics.mpi-bn.mpg.de) that allows access and queries to the database without prior bioinformatical expertise. The repository is updated regularly, incorporating new published datasets from omics technologies.

  5. "Omics" of maize stress response for sustainable food production: opportunities and challenges.

    Science.gov (United States)

    Gong, Fangping; Yang, Le; Tai, Fuju; Hu, Xiuli; Wang, Wei

    2014-12-01

    Maize originated in the highlands of Mexico approximately 8700 years ago and is one of the most commonly grown cereal crops worldwide, followed by wheat and rice. Abiotic stresses (primarily drought, salinity, and high and low temperatures), together with biotic stresses (primarily fungi, viruses, and pests), negatively affect maize growth, development, and eventually production. To understand the response of maize to abiotic and biotic stresses and its mechanism of stress tolerance, high-throughput omics approaches have been used in maize stress studies. Integrated omics approaches are crucial for dissecting the temporal and spatial system-level changes that occur in maize under various stresses. In this comprehensive analysis, we review the primary types of stresses that threaten sustainable maize production; underscore the recent advances in maize stress omics, especially proteomics; and discuss the opportunities, challenges, and future directions of maize stress omics, with a view to sustainable food production. The knowledge gained from studying maize stress omics is instrumental for improving maize to cope with various stresses and to meet the food demands of the exponentially growing global population. Omics systems science offers actionable potential solutions for sustainable food production, and we present maize as a notable case study.

  6. 'Omic' genetic technologies for herbal medicines in psychiatry.

    Science.gov (United States)

    Sarris, Jerome; Ng, Chee Hong; Schweitzer, Isaac

    2012-04-01

    The field of genetics, which includes the use of 'omic' technologies, is an evolving area of science that has emerging application in phytotherapy. Omic studies include pharmacogenomics, proteomics and metabolomics. Herbal medicines, as monotherapies, or complex formulations such as traditional Chinese herbal prescriptions, may benefit from omic studies, and this new field may be termed 'herbomics'. Applying herbomics in the field of psychiatry may provide answers about which herbal interventions may be effective for individuals, which genetic processes are triggered, and the subsequent neurochemical pathways of activity. The use of proteomic technology can explore the differing epigenetic effects on neurochemical gene expression between individual herbs, isolated constituents and complex formulae. The possibilities of side effects or insufficient response to the herb can also be assessed via pharmacogenomic analysis of polymorphisms of cytochrome P450 liver enzymes or P-glycoprotein. While another novel application of omic technology is for the validation of the concept of synergy in individual herbal extracts and prescriptive formulations. Chronic administration of psychotropic herbal medicines may discover important effects on chromatin remodelling via modification of histone and DNA methylation. This paper focuses on the emerging field of herbomics, and is to our knowledge the first publication to explore this in the area of psychiatry. Copyright © 2011 John Wiley & Sons, Ltd.

  7. Establishing multiple omics baselines for three Southeast Asian populations in the Singapore Integrative Omics Study.

    Science.gov (United States)

    Saw, Woei-Yuh; Tantoso, Erwin; Begum, Husna; Zhou, Lihan; Zou, Ruiyang; He, Cheng; Chan, Sze Ling; Tan, Linda Wei-Lin; Wong, Lai-Ping; Xu, Wenting; Moong, Don Kyin Nwe; Lim, Yenly; Li, Bowen; Pillai, Nisha Esakimuthu; Peterson, Trevor A; Bielawny, Tomasz; Meikle, Peter J; Mundra, Piyushkumar A; Lim, Wei-Yen; Luo, Ma; Chia, Kee-Seng; Ong, Rick Twee-Hee; Brunham, Liam R; Khor, Chiea-Chuen; Too, Heng Phon; Soong, Richie; Wenk, Markus R; Little, Peter; Teo, Yik-Ying

    2017-09-21

    The Singapore Integrative Omics Study provides valuable insights on establishing population reference measurement in 364 Chinese, Malay, and Indian individuals. These measurements include > 2.5 millions genetic variants, 21,649 transcripts expression, 282 lipid species quantification, and 284 clinical, lifestyle, and dietary variables. This concept paper introduces the depth of the data resource, and investigates the extent of ethnic variation at these omics and non-omics biomarkers. It is evident that there are specific biomarkers in each of these platforms to differentiate between the ethnicities, and intra-population analyses suggest that Chinese and Indians are the most biologically homogeneous and heterogeneous, respectively, of the three groups. Consistent patterns of correlations between lipid species also suggest the possibility of lipid tagging to simplify future lipidomics assays. The Singapore Integrative Omics Study is expected to allow the characterization of intra-omic and inter-omic correlations within and across all three ethnic groups through a systems biology approach.The Singapore Genome Variation projects characterized the genetics of Singapore's Chinese, Malay, and Indian populations. The Singapore Integrative Omics Study introduced here goes further in providing multi-omic measurements in individuals from these populations, including genetic, transcriptome, lipidome, and lifestyle data, and will facilitate the study of common diseases in Asian communities.

  8. Big Data, epistemology and causality: Knowledge in and knowledge out in EXPOsOMICS

    Directory of Open Access Journals (Sweden)

    Stefano Canali

    2016-09-01

    Full Text Available Recently, it has been argued that the use of Big Data transforms the sciences, making data-driven research possible and studying causality redundant. In this paper, I focus on the claim on causal knowledge by examining the Big Data project EXPOsOMICS, whose research is funded by the European Commission and considered capable of improving our understanding of the relation between exposure and disease. While EXPOsOMICS may seem the perfect exemplification of the data-driven view, I show how causal knowledge is necessary for the project, both as a source for handling complexity and as an output for meeting the project’s goals. Consequently, I argue that data-driven claims about causality are fundamentally flawed and causal knowledge should be considered a necessary aspect of Big Data science. In addition, I present the consequences of this result on other data-driven claims, concerning the role of theoretical considerations. I argue that the importance of causal knowledge and other kinds of theoretical engagement in EXPOsOMICS undermine theory-free accounts and suggest alternative ways of framing science based on Big Data.

  9. Proceedings of RIKEN BNL Research Center Workshop: The Approach to Equilibrium in Strongly Interacting Matter. Volume 118

    Energy Technology Data Exchange (ETDEWEB)

    Liao, J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Venugopalan, R. [Brookhaven National Lab. (BNL), Upton, NY (United States); Berges, J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Blaizot, J. -P. [Brookhaven National Lab. (BNL), Upton, NY (United States); Gelis, F. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2014-04-09

    The RIKEN BNL Research Center (RBRC) was established in April 1997 at Brookhaven National Laboratory*. It is funded by the ''Rikagaku Kenkyusho'' (RIKEN, The Institute of Physical and Chemical Research) of Japan and the U. S. Department of Energy’s Office of Science. The RBRC is dedicated to the study of strong interactions, including spin physics, lattice QCD, and RHIC physics through the nurturing of a new generation of young physicists. The RBRC has theory, lattice gauge computing and experimental components. It is presently exploring the possibility of an astrophysics component being added to the program. The purpose of this Workshop is to critically review the recent progress on the theory and phenomenology of early time dynamics in relativistic heavy ion collisions from RHIC to LHC energies, to examine the various approaches on thermalization and existing issues, and to formulate new research efforts for the future. Topics slated to be covered include Experimental evidence for equilibration/isotropization, comparison of various approaches, dependence on the initial conditions and couplings, and turbulent cascades and Bose-Einstein condensation.

  10. CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002.

    Science.gov (United States)

    Yang, Yaohua; Feng, Jie; Li, Tao; Ge, Feng; Zhao, Jindong

    2015-01-01

    Cyanobacteria are an important group of organisms that carry out oxygenic photosynthesis and play vital roles in both the carbon and nitrogen cycles of the Earth. The annotated genome of Synechococcus sp. PCC 7002, as an ideal model cyanobacterium, is available. A series of transcriptomic and proteomic studies of Synechococcus sp. PCC 7002 cells grown under different conditions have been reported. However, no database of such integrated omics studies has been constructed. Here we present CyanOmics, a database based on the results of Synechococcus sp. PCC 7002 omics studies. CyanOmics comprises one genomic dataset, 29 transcriptomic datasets and one proteomic dataset and should prove useful for systematic and comprehensive analysis of all those data. Powerful browsing and searching tools are integrated to help users directly access information of interest with enhanced visualization of the analytical results. Furthermore, Blast is included for sequence-based similarity searching and Cluster 3.0, as well as the R hclust function is provided for cluster analyses, to increase CyanOmics's usefulness. To the best of our knowledge, it is the first integrated omics analysis database for cyanobacteria. This database should further understanding of the transcriptional patterns, and proteomic profiling of Synechococcus sp. PCC 7002 and other cyanobacteria. Additionally, the entire database framework is applicable to any sequenced prokaryotic genome and could be applied to other integrated omics analysis projects. Database URL: http://lag.ihb.ac.cn/cyanomics. © The Author(s) 2015. Published by Oxford University Press.

  11. Proceedings of RIKEN BNL Research Center Workshop, Volume 91, RBRC Scientific Review Committee Meeting

    Energy Technology Data Exchange (ETDEWEB)

    Samios,N.P.

    2008-11-17

    The ninth evaluation of the RIKEN BNL Research Center (RBRC) took place on Nov. 17-18, 2008, at Brookhaven National Laboratory. The members of the Scientific Review Committee (SRC) were Dr. Dr. Wit Busza (Chair), Dr. Miklos Gyulassy, Dr. Akira Masaike, Dr. Richard Milner, Dr. Alfred Mueller, and Dr. Akira Ukawa. We are pleased that Dr. Yasushige Yano, the Director of the Nishina Institute of RIKEN, Japan participated in this meeting both in informing the committee of the activities of the Nishina Institute and the role of RBRC and as an observer of this review. In order to illustrate the breadth and scope of the RBRC program, each member of the Center made a presentation on his/her research efforts. This encompassed three major areas of investigation, theoretical, experimental and computational physics. In addition the committee met privately with the fellows and postdocs to ascertain their opinions and concerns. Although the main purpose of this review is a report to RIKEN Management (Dr. Ryoji Noyori, RIKEN President) on the health, scientific value, management and future prospects of the Center, the RBRC management felt that a compendium of the scientific presentations are of sufficient quality and interest that they warrant a wider distribution. Therefore we have made this compilation and present it to the community for its information and enlightenment.

  12. EXPOsOMICS: final policy workshop and stakeholder consultation.

    Science.gov (United States)

    Turner, Michelle C; Vineis, Paolo; Seleiro, Eduardo; Dijmarescu, Michaela; Balshaw, David; Bertollini, Roberto; Chadeau-Hyam, Marc; Gant, Timothy; Gulliver, John; Jeong, Ayoung; Kyrtopoulos, Soterios; Martuzzi, Marco; Miller, Gary W; Nawrot, Timothy; Nieuwenhuijsen, Mark; Phillips, David H; Probst-Hensch, Nicole; Samet, Jonathan; Vermeulen, Roel; Vlaanderen, Jelle; Vrijheid, Martine; Wild, Christopher; Kogevinas, Manolis

    2018-02-15

    The final meeting of the EXPOsOMICS project "Final Policy Workshop and Stakeholder Consultation" took place 28-29 March 2017 to present the main results of the project and discuss their implications both for future research and for regulatory and policy activities. This paper summarizes presentations and discussions at the meeting related with the main results and advances in exposome research achieved through the EXPOsOMICS project; on other parallel research initiatives on the study of the exposome in Europe and in the United States and their complementarity to EXPOsOMICS; lessons learned from these early studies on the exposome and how they may shape the future of research on environmental exposure assessment; and finally the broader implications of exposome research for risk assessment and policy development on environmental exposures. The main results of EXPOsOMICS in relation to studies of the external exposome and internal exposome in relation to both air pollution and water contaminants were presented as well as new technologies for environmental health research (adductomics) and advances in statistical methods. Although exposome research strengthens the scientific basis for policy development, there is a need in terms of showing added value for public health to: improve communication of research results to non-scientific audiences; target research to the broader landscape of societal challenges; and draw applicable conclusions. Priorities for future work include the development and standardization of methodologies and technologies for assessing the external and internal exposome, improved data sharing and integration, and the demonstration of the added value of exposome science over conventional approaches in answering priority policy questions.

  13. [Progress in omics research of Aspergillus niger].

    Science.gov (United States)

    Sui, Yufei; Ouyang, Liming; Lu, Hongzhong; Zhuang, Yingping; Zhang, Siliang

    2016-08-25

    Aspergillus niger, as an important industrial fermentation strain, is widely applied in the production of organic acids and industrial enzymes. With the development of diverse omics technologies, the data of genome, transcriptome, proteome and metabolome of A. niger are increasing continuously, which declared the coming era of big data for the research in fermentation process of A. niger. The data analysis from single omics and the comparison of multi-omics, to the integrations of multi-omics based on the genome-scale metabolic network model largely extends the intensive and systematic understanding of the efficient production mechanism of A. niger. It also provides possibilities for the reasonable global optimization of strain performance by genetic modification and process regulation. We reviewed and summarized progress in omics research of A. niger, and proposed the development direction of omics research on this cell factory.

  14. Advancing stroke genomic research in the age of Trans-Omics big data science: Emerging priorities and opportunities.

    Science.gov (United States)

    Owolabi, Mayowa; Peprah, Emmanuel; Xu, Huichun; Akinyemi, Rufus; Tiwari, Hemant K; Irvin, Marguerite R; Wahab, Kolawole Wasiu; Arnett, Donna K; Ovbiagele, Bruce

    2017-11-15

    We systematically reviewed the genetic variants associated with stroke in genome-wide association studies (GWAS) and examined the emerging priorities and opportunities for rapidly advancing stroke research in the era of Trans-Omics science. Using the PRISMA guideline, we searched PubMed and NHGRI- EBI GWAS catalog for stroke studies from 2007 till May 2017. We included 31 studies. The major challenge is that the few validated variants could not account for the full genetic risk of stroke and have not been translated for clinical use. None of the studies included continental Africans. Genomic study of stroke among Africans presents a unique opportunity for the discovery, validation, functional annotation, Trans-Omics study and translation of genomic determinants of stroke with implications for global populations. This is because all humans originated from Africa, a continent with a unique genomic architecture and a distinctive epidemiology of stroke; as well as substantially higher heritability and resolution of fine mapping of stroke genes. Understanding the genomic determinants of stroke and the corresponding molecular mechanisms will revolutionize the development of a new set of precise biomarkers for stroke prediction, diagnosis and prognostic estimates as well as personalized interventions for reducing the global burden of stroke. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. GeneLab: A Systems Biology Platform for Spaceflight Omics Data

    Science.gov (United States)

    Reinsch, Sigrid S.; Lai, San-Huei; Chen, Rick; Thompson, Terri; Berrios, Daniel; Fogle, Homer; Marcu, Oana; Timucin, Linda; Chakravarty, Kaushik; Coughlan, Joseph

    2015-01-01

    NASA's mission includes expanding our understanding of biological systems to improve life on Earth and to enable long-duration human exploration of space. Resources to support large numbers of spaceflight investigations are limited. NASA's GeneLab project is maximizing the science output from these experiments by: (1) developing a unique public bioinformatics database that includes space bioscience relevant "omics" data (genomics, transcriptomics, proteomics, and metabolomics) and experimental metadata; (2) partnering with NASA-funded flight experiments through bio-sample sharing or sample augmentation to expedite omics data input to the GeneLab database; and (3) developing community-driven reference flight experiments. The first database, GeneLab Data System Version 1.0, went online in April 2015. V1.0 contains numerous flight datasets and has search and download capabilities. Version 2.0 will be released in 2016 and will link to analytic tools. In 2015 Genelab partnered with two Biological Research in Canisters experiments (BBRIC-19 and BRIC-20) which examine responses of Arabidopsis thaliana to spaceflight. GeneLab also partnered with Rodent Research-1 (RR1), the maiden flight to test the newly developed rodent habitat. GeneLab developed protocols for maxiumum yield of RNA, DNA and protein from precious RR-1 tissues harvested and preserved during the SpaceX-4 mission, as well as from tissues from mice that were frozen intact during spaceflight and later dissected. GeneLab is establishing partnerships with at least three planned flights for 2016. Organism-specific nationwide Science Definition Teams (SDTs) will define future GeneLab dedicated missions and ensure the broader scientific impact of the GeneLab missions. GeneLab ensures prompt release and open access to all high-throughput omics data from spaceflight and ground-based simulations of microgravity and radiation. Overall, GeneLab will facilitate the generation and query of parallel multi-omics data, and

  16. Omics AnalySIs System for PRecision Oncology (OASISPRO): A Web-based Omics Analysis Tool for Clinical Phenotype Prediction.

    Science.gov (United States)

    Yu, Kun-Hsing; Fitzpatrick, Michael R; Pappas, Luke; Chan, Warren; Kung, Jessica; Snyder, Michael

    2017-09-12

    Precision oncology is an approach that accounts for individual differences to guide cancer management. Omics signatures have been shown to predict clinical traits for cancer patients. However, the vast amount of omics information poses an informatics challenge in systematically identifying patterns associated with health outcomes, and no general-purpose data-mining tool exists for physicians, medical researchers, and citizen scientists without significant training in programming and bioinformatics. To bridge this gap, we built the Omics AnalySIs System for PRecision Oncology (OASISPRO), a web-based system to mine the quantitative omics information from The Cancer Genome Atlas (TCGA). This system effectively visualizes patients' clinical profiles, executes machine-learning algorithms of choice on the omics data, and evaluates the prediction performance using held-out test sets. With this tool, we successfully identified genes strongly associated with tumor stage, and accurately predicted patients' survival outcomes in many cancer types, including mesothelioma and adrenocortical carcinoma. By identifying the links between omics and clinical phenotypes, this system will facilitate omics studies on precision cancer medicine and contribute to establishing personalized cancer treatment plans. This web-based tool is available at http://tinyurl.com/oasispro ;source codes are available at http://tinyurl.com/oasisproSourceCode . © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  17. Omics strategies for revealing Yersinia pestis virulence

    Science.gov (United States)

    Yang, Ruifu; Du, Zongmin; Han, Yanping; Zhou, Lei; Song, Yajun; Zhou, Dongsheng; Cui, Yujun

    2012-01-01

    Omics has remarkably changed the way we investigate and understand life. Omics differs from traditional hypothesis-driven research because it is a discovery-driven approach. Mass datasets produced from omics-based studies require experts from different fields to reveal the salient features behind these data. In this review, we summarize omics-driven studies to reveal the virulence features of Yersinia pestis through genomics, trascriptomics, proteomics, interactomics, etc. These studies serve as foundations for further hypothesis-driven research and help us gain insight into Y. pestis pathogenesis. PMID:23248778

  18. Clustering multilayer omics data using MuNCut.

    Science.gov (United States)

    Teran Hidalgo, Sebastian J; Ma, Shuangge

    2018-03-14

    Omics profiling is now a routine component of biomedical studies. In the analysis of omics data, clustering is an essential step and serves multiple purposes including for example revealing the unknown functionalities of omics units, assisting dimension reduction in outcome model building, and others. In the most recent omics studies, a prominent trend is to conduct multilayer profiling, which collects multiple types of genetic, genomic, epigenetic and other measurements on the same subjects. In the literature, clustering methods tailored to multilayer omics data are still limited. Directly applying the existing clustering methods to multilayer omics data and clustering each layer first and then combing across layers are both "suboptimal" in that they do not accommodate the interconnections within layers and across layers in an informative way. In this study, we develop the MuNCut (Multilayer NCut) clustering approach. It is tailored to multilayer omics data and sufficiently accounts for both across- and within-layer connections. It is based on the novel NCut technique and also takes advantages of regularized sparse estimation. It has an intuitive formulation and is computationally very feasible. To facilitate implementation, we develop the function muncut in the R package NcutYX. Under a wide spectrum of simulation settings, it outperforms competitors. The analysis of TCGA (The Cancer Genome Atlas) data on breast cancer and cervical cancer shows that MuNCut generates biologically meaningful results which differ from those using the alternatives. We propose a more effective clustering analysis of multiple omics data. It provides a new venue for jointly analyzing genetic, genomic, epigenetic and other measurements.

  19. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP, VOLUME 66

    International Nuclear Information System (INIS)

    OGAWA, A.

    2005-01-01

    The RIKEN BNL Research Center (RSRC) was established in April 1997 at Brookhaven National Laboratory. It is funded by the 'Rikagaku Kenkyusho (RIKEN, The Institute of Physical and Chemical Research) of Japan. The Center is dedicated to the study of strong interactions, including spin physics, lattice QCD, and RHIC physics through the nurturing of a new generation of young physicists. The RBRC has both a theory and experimental component. At present the theoretical group has 4 Fellows and 3 Research Associates as well as 11 RHIC Physics/University Fellows (academic year 2003-2004). To date there are approximately 30 graduates from the program of which 13 have attained tenure positions at major institutions worldwide. The experimental group is smaller and has 2 Fellows and 3 RHIC Physics/University Fellows and 3 Research Associates, and historically 6 individuals have attained permanent positions. Beginning in 2001 a new RIKEN Spin Program (RSP) category was implemented at RBRC. These appointments are joint positions of RBRC and RIKEN and include the following positions in theory and experiment: RSP Researchers, RSP Research Associates, and Young Researchers, who are mentored by senior RBRC Scientists, A number of RIKEN Jr. Research Associates and Visiting Scientists also contribute to the physics program at the Center. RBRC has an active workshop program on strong interaction physics with each workshop focused on a specific physics problem. Each workshop speaker is encouraged to select a few of the most important transparencies from his or her presentation, accompanied by a page of explanation. This material is collected at the end of the workshop by the organizer to form proceedings, which can therefore be available within a short time. To date there are sixty nine proceedings volumes available. The construction of a 0.6 teraflops parallel processor, dedicated to lattice QCD, begun at the Center on February 19, 1998, was completed on August 28, 1998 and is still

  20. Superheavy research at RIKEN

    International Nuclear Information System (INIS)

    Morita, Kosuke

    2010-01-01

    At RIKEN, Japan, we performed experiments to study the productions and decays of the heaviest elements produced by 208 Pb- and 209 Bi- based 'cold fusion' reactions. A gas-filled recoil separator GARIS was used for the study. In the study of 209 Bi( 70 Zn, n) reaction, we observed two decay chains originating from an isotope of the 113th element, 178 113, which were assigned firstly by generic correlation of the alpha decay chains connected into the previously known decay of 266 Bh and 262 Db via previously unknown alpha decays of 278 113, 274 Rg, and 270 Mt. In addition, decay properties of an isotope 266 Bh and its daughter nucleus 262 Db produced by the 248 Cm( 23 Na, 5n) reaction were studied. 266 Bh was clearly identified from the correlation of the known nuclide, 262 Db, providing further confirmation of the discovery of 278 113.

  1. Use of Free/Libre Open Source Software in Sepsis "-Omics" Research: A Bibliometric, Comparative Analysis Among the United States, EU-28 Member States, and China.

    Science.gov (United States)

    Evangelatos, Nikolaos; Satyamourthy, Kapaettu; Levidou, Georgia; Brand, Helmut; Bauer, Pia; Kouskouti, Christina; Brand, Angela

    2018-05-01

    "-Omics" systems sciences are at the epicenter of personalized medicine and public health, and drivers of knowledge-based biotechnology innovation. Bioinformatics, a core component of omics research, is one of the disciplines that first employed Free/Libre Open Source Software (FLOSS), and thus provided a fertile ground for its further development. Understanding the use and characteristics of FLOSS deployed in the omics field is valuable for future innovation strategies, policy and funding priorities. We conducted a bibliometric, longitudinal study of the use of FLOSS in sepsis omics research from 2011 to 2015 in the United States, EU-28 and China. Because sepsis is an interdisciplinary field at the intersection of multiple omics technologies and medical specialties, it was chosen as a model innovation ecosystem for this empirical analysis, which used publicly available data. Despite development of and competition from proprietary commercial software, scholars in omics continue to employ FLOSS routinely, and independent of the type of omics technology they work with. The number of articles using FLOSS increased significantly over time in the EU-28, as opposed to the United States and China (R = 0.96, p = 0.004). Furthermore, in an era where sharing of knowledge is being strongly advocated and promoted by public agencies and social institutions, we discuss possible correlations between the use of FLOSS and various funding sources in omics research. These observations and analyses provide new insights into the use of FLOSS in sepsis omics research across three (supra)national regions. Further benchmarking studies are warranted for FLOSS trends in other omics fields and geographical settings. These could, in time, lead to the development of new composite innovation and technology use metrics in omics systems sciences and bioinformatics communities.

  2. Multi-Omics Research Trends in Sepsis: A Bibliometric, Comparative Analysis Between the United States, the European Union 28 Member States, and China.

    Science.gov (United States)

    Evangelatos, Nikolaos; Satyamoorthy, Kapaettu; Levidou, Georgia; Bauer, Pia; Brand, Helmut; Kouskouti, Christina; Lehrach, Hans; Brand, Angela

    2018-03-01

    "-Omics" research is in transition with the recent rise of multi-omics technology platforms. Integration of "-omics" and multi-omics research is of high priority in sepsis, a heterogeneous syndrome that is widely recognized as a global health burden and a priority biomedical funding field. We report here an original study on bibliometric trends in the use of "-omics" technologies, and multi-omics approaches in particular, in sepsis research in three (supra)national settings, the United States, the European Union 28 Member States (EU-28), and China. Using a 5-year longitudinal bibliometric study design from 2011 to 2015, we analyzed the sepsis-related research articles in English language that included at least one or multi-omics technologies in publicly available form in Medline (free full texts). We found that the United States has had the lead (almost one-third of publications) in the inclusion of an "-omics" or multi-omics technology in sepsis within the study period. However, both China and the EU-28 displayed a significant increase in the number of publications that employed one or more types of "-omics" research (p < 0.005), while the EU-28 displayed a significant increase especially in multi-omics research articles in sepsis (p < 0.05). Notably, more than half of the multi-omics research studies in the sepsis knowledge domain had a university or government/state funding source. Among the multi-omics research publications in sepsis, the combination of genomics and transcriptomics was the most frequent (40.5%), followed by genomics and proteomics (20.4%). We suggest that the lead of the United States in the field of "-omics" and multi-omics research in sepsis is likely at stake, with both the EU-28 and China rapidly increasing their research capacity. Moreover, "triple omics" that combine genomics, proteomics, and metabolomics analyses appear to be uncommon in sepsis, and yet much needed for triangulation of systems science data. These observations

  3. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP, VOLUME 72, RHIC SPIN COLLABORATION MEETINGS XXXI, XXXII, XXXIII

    International Nuclear Information System (INIS)

    OGAWA, A.

    2005-01-01

    The RIKEN BNL Research Center (RBRC) was established in April 1997 at Brookhaven National Laboratory. It is funded by the ''Rikagaku Kenkyusho'' (RIKEN, The Institute of Physical and Chemical Research) of Japan. The Center is dedicated to the study of strong interactions, including spin physics, lattice QCD, and RHIC physics through the nurturing of a new generation of young physicists. The RBRC has both a theory and experimental component. At present the theoretical group has 4 Fellows and 3 Research Associates as well as 11 RHIC Physics/University Fellows (academic year 2003-2004). To date there are approximately 30 graduates from the program of which 13 have attained tenure positions at major institutions worldwide. The experimental group is smaller and has 2 Fellows and 3 RHIC Physics/University Fellows and 3 Research Associates, and historically 6 individuals have attained permanent positions. Beginning in 2001 a new RIKEN Spin Program (RSP) category was implemented at RBRC. These appointments are joint positions of RBRC and RIKEN and include the following positions in theory and experiment: RSP Researchers, RSP Research Associates, and Young Researchers, who are mentored by senior RBRC Scientists. A number of RIKEN Jr. Research Associates and Visiting Scientists also contribute to the physics program at the Center. RBRC has an active workshop program on strong interaction physics with each workshop focused on a specific physics problem. Each workshop speaker is encouraged to select a few of the most important transparencies from his or her presentation, accompanied by a page of explanation. This material is collected at the end of the workshop by the organizer to form proceedings, which can therefore be available within a short time. To date there are seventy-two proceeding volumes available. The construction of a 0.6 teraflops parallel processor, dedicated to lattice QCD, begun at the Center on February 19, 1998, was completed on August 28, 1998 and is still

  4. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP, VOLUME 77, RBRC SCIENTIFIC REVIEW COMMITTEE MEETING, OCTOBER 10-12, 2005

    International Nuclear Information System (INIS)

    SAMIOS, N.P.

    2005-01-01

    The eighth evaluation of the RIKEN BNL Research Center (RBRC) took place on October 10-12, 2005, at Brookhaven National Laboratory. The members of the Scientific Review Committee (SRC) were Dr. Jean-Paul Blaizot, Professor Makoto Kobayashi, Dr. Akira Masaike, Professor Charles Young Prescott (Chair), Professor Stephen Sharpe (absent), and Professor Jack Sandweiss. We are grateful to Professor Akira Ukawa who was appointed to the SRC to cover Professor Sharpe's area of expertise. In addition to reviewing this year's program, the committee, augmented by Professor Kozi Nakai, evaluated the RBRC proposal for a five-year extension of the RIKEN BNL Collaboration MOU beyond 2007. Dr. Koji Kaya, Director of the Discovery Research Institute, RIKEN, Japan, presided over the session on the extension proposal. In order to illustrate the breadth and scope of the RBRC program, each member of the Center made a presentation on higher research efforts. In addition, a special session was held in connection with the RBRC QCDSP and QCDOC supercomputers. Professor Norman H. Christ, a collaborator from Columbia University, gave a presentation on the progress and status of the project, and Professor Frithjof Karsch of BNL presented the first physics results from QCDOC. Although the main purpose of this review is a report to RIKEN Management (Dr. Ryoji Noyori, RIKEN President) on the health, scientific value, management and future prospects of the Center, the RBRC management felt that a compendium of the scientific presentations are of sufficient quality and interest that they warrant a wider distribution. Therefore we have made this compilation and present it to the community for its information and enlightenment

  5. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP, VOLUME 77, RBRC SCIENTIFIC REVIEW COMMITTEE MEETING, OCTOBER 10-12, 2005

    Energy Technology Data Exchange (ETDEWEB)

    SAMIOS, N.P.

    2005-10-10

    The eighth evaluation of the RIKEN BNL Research Center (RBRC) took place on October 10-12, 2005, at Brookhaven National Laboratory. The members of the Scientific Review Committee (SRC) were Dr. Jean-Paul Blaizot, Professor Makoto Kobayashi, Dr. Akira Masaike, Professor Charles Young Prescott (Chair), Professor Stephen Sharpe (absent), and Professor Jack Sandweiss. We are grateful to Professor Akira Ukawa who was appointed to the SRC to cover Professor Sharpe's area of expertise. In addition to reviewing this year's program, the committee, augmented by Professor Kozi Nakai, evaluated the RBRC proposal for a five-year extension of the RIKEN BNL Collaboration MOU beyond 2007. Dr. Koji Kaya, Director of the Discovery Research Institute, RIKEN, Japan, presided over the session on the extension proposal. In order to illustrate the breadth and scope of the RBRC program, each member of the Center made a presentation on higher research efforts. In addition, a special session was held in connection with the RBRC QCDSP and QCDOC supercomputers. Professor Norman H. Christ, a collaborator from Columbia University, gave a presentation on the progress and status of the project, and Professor Frithjof Karsch of BNL presented the first physics results from QCDOC. Although the main purpose of this review is a report to RIKEN Management (Dr. Ryoji Noyori, RIKEN President) on the health, scientific value, management and future prospects of the Center, the RBRC management felt that a compendium of the scientific presentations are of sufficient quality and interest that they warrant a wider distribution. Therefore we have made this compilation and present it to the community for its information and enlightenment.

  6. RIKEN RI Beam Factory project

    Energy Technology Data Exchange (ETDEWEB)

    Yano, Yasushige; Goto, Akira; Katayama, Takeshi [Institute of Physical and Chemical Research, Wako, Saitama (Japan)

    1997-03-01

    The RARF proposes `RIKEN RI Beam Factory` as a next facility-expanding project. The factory makes it the primary aim to provide RI (Radioactive Isotope) beams covering over the whole atomic-mass range with the world-highest intensity in a wide energy range up to several hundreds MeV/nucleon. These RI beams are generated by the fragmentation of high-intensity heavy-ion beams. For the efficient production heavy-ion energies will be boosted up to over 100 MeV/nucleon even for very heavy ions by a K2500-MeV superconducting ring cyclotron serving as a post accelerator of the existing K540-MeV ring cyclotron. A new type of experimental installation called `MUSES` (Multi-USe Experimental Storage rings) will be constructed as well. With MUSES, various types of unique colliding experiments will become possible. (author)

  7. Differential Expression and Functional Analysis of High-Throughput -Omics Data Using Open Source Tools.

    Science.gov (United States)

    Kebschull, Moritz; Fittler, Melanie Julia; Demmer, Ryan T; Papapanou, Panos N

    2017-01-01

    Today, -omics analyses, including the systematic cataloging of messenger RNA and microRNA sequences or DNA methylation patterns in a cell population, organ, or tissue sample, allow for an unbiased, comprehensive genome-level analysis of complex diseases, offering a large advantage over earlier "candidate" gene or pathway analyses. A primary goal in the analysis of these high-throughput assays is the detection of those features among several thousand that differ between different groups of samples. In the context of oral biology, our group has successfully utilized -omics technology to identify key molecules and pathways in different diagnostic entities of periodontal disease.A major issue when inferring biological information from high-throughput -omics studies is the fact that the sheer volume of high-dimensional data generated by contemporary technology is not appropriately analyzed using common statistical methods employed in the biomedical sciences.In this chapter, we outline a robust and well-accepted bioinformatics workflow for the initial analysis of -omics data generated using microarrays or next-generation sequencing technology using open-source tools. Starting with quality control measures and necessary preprocessing steps for data originating from different -omics technologies, we next outline a differential expression analysis pipeline that can be used for data from both microarray and sequencing experiments, and offers the possibility to account for random or fixed effects. Finally, we present an overview of the possibilities for a functional analysis of the obtained data.

  8. Stepping into the omics era: Opportunities and challenges for biomaterials science and engineering☆

    Science.gov (United States)

    Rabitz, Herschel; Welsh, William J.; Kohn, Joachim; de Boer, Jan

    2016-01-01

    The research paradigm in biomaterials science and engineering is evolving from using low-throughput and iterative experimental designs towards high-throughput experimental designs for materials optimization and the evaluation of materials properties. Computational science plays an important role in this transition. With the emergence of the omics approach in the biomaterials field, referred to as materiomics, high-throughput approaches hold the promise of tackling the complexity of materials and understanding correlations between material properties and their effects on complex biological systems. The intrinsic complexity of biological systems is an important factor that is often oversimplified when characterizing biological responses to materials and establishing property-activity relationships. Indeed, in vitro tests designed to predict in vivo performance of a given biomaterial are largely lacking as we are not able to capture the biological complexity of whole tissues in an in vitro model. In this opinion paper, we explain how we reached our opinion that converging genomics and materiomics into a new field would enable a significant acceleration of the development of new and improved medical devices. The use of computational modeling to correlate high-throughput gene expression profiling with high throughput combinatorial material design strategies would add power to the analysis of biological effects induced by material properties. We believe that this extra layer of complexity on top of high-throughput material experimentation is necessary to tackle the biological complexity and further advance the biomaterials field. PMID:26876875

  9. Omics Informatics: From Scattered Individual Software Tools to Integrated Workflow Management Systems.

    Science.gov (United States)

    Ma, Tianle; Zhang, Aidong

    2017-01-01

    Omic data analyses pose great informatics challenges. As an emerging subfield of bioinformatics, omics informatics focuses on analyzing multi-omic data efficiently and effectively, and is gaining momentum. There are two underlying trends in the expansion of omics informatics landscape: the explosion of scattered individual omics informatics tools with each of which focuses on a specific task in both single- and multi- omic settings, and the fast-evolving integrated software platforms such as workflow management systems that can assemble multiple tools into pipelines and streamline integrative analysis for complicated tasks. In this survey, we give a holistic view of omics informatics, from scattered individual informatics tools to integrated workflow management systems. We not only outline the landscape and challenges of omics informatics, but also sample a number of widely used and cutting-edge algorithms in omics data analysis to give readers a fine-grained view. We survey various workflow management systems (WMSs), classify them into three levels of WMSs from simple software toolkits to integrated multi-omic analytical platforms, and point out the emerging needs for developing intelligent workflow management systems. We also discuss the challenges, strategies and some existing work in systematic evaluation of omics informatics tools. We conclude by providing future perspectives of emerging fields and new frontiers in omics informatics.

  10. Assessment of berberine as a multi-target antimicrobial: a multi-omics study for drug discovery and repositioning.

    Science.gov (United States)

    Karaosmanoglu, Kubra; Sayar, Nihat Alpagu; Kurnaz, Isil Aksan; Akbulut, Berna Sariyar

    2014-01-01

    Postgenomics drug development is undergoing major transformation in the age of multi-omics studies and drug repositioning. Rather than applications solely in personalized medicine, omics science thus additionally offers a better understanding of a broader range of drug targets and drug repositioning. Berberine is an isoquinoline alkaloid found in many medicinal plants. We report here a whole genome microarray study in tandem with proteomics techniques for mining the plethora of targets that are putatively involved in the antimicrobial activity of berberine against Escherichia coli. We found DNA replication/repair and transcription to be triggered by berberine, indicating that nucleic acids, in general, are among its targets. Our combined transcriptomics and proteomics multi-omics findings underscore that, in the presence of berberine, cell wall or cell membrane transport and motility-related functions are also specifically regulated. We further report a general decline in metabolism, as seen by repression of genes in carbohydrate and amino acid metabolism, energy production, and conversion. An involvement of multidrug efflux pumps, as well as reduced membrane permeability for developing resistance against berberine in E. coli was noted. Collectively, these findings offer original and significant leads for omics-guided drug discovery and future repositioning approaches in the postgenomics era, using berberine as a multi-omics case study.

  11. Utilization of Different Omic Approaches to Unravel Stress Response Mechanisms in the Parasite Entamoeba histolytica

    Directory of Open Access Journals (Sweden)

    Shruti Nagaraja

    2018-02-01

    Full Text Available During its life cycle, the unicellular parasite Entamoeba histolytica is challenged by a wide variety of environmental stresses, such as fluctuation in glucose concentration, changes in gut microbiota composition, and the release of oxidative and nitrosative species from neutrophils and macrophages. The best mode of survival for this parasite is to continuously adapt itself to the dynamic environment of the host. Our ability to study the stress-induced responses and adaptive mechanisms of this parasite has been transformed through the development of genomics, proteomics or metabolomics (omics sciences. These studies provide insights into different facets of the parasite's behavior in the host. However, there is a dire need for multi-omics data integration to better understand its pathogenic nature, ultimately paving the way to identify new chemotherapeutic targets against amebiasis. This review provides an integration of the most relevant omics information on the mechanisms that are used by E. histolytica to resist environmental stresses.

  12. Omics and cachexia.

    Science.gov (United States)

    Twelkmeyer, Brigitte; Tardif, Nicolas; Rooyackers, Olav

    2017-05-01

    The purpose of this review is to recapture recent advances in cachexia-related diseases, mainly cancer cachexia, and treatment using genomic, transcriptomics, proteomic, and metabolomics-related techniques. From recent studies in the cancer cachexia field it is clear that the tumor has a direct effect on distant organs via its secretome. The affected pathways on the other hand were largely known from earlier studies with changes in energy-related pathways (mainly lipid metabolism) and the protein degradation pathways. Treatment-oriented studies use mostly rodent models and in-vivo cultures and it is too early for human studies. Omics tools are powerful if used in the right way. Omics research has identified the tumor as an important player in cancer cachexia and some interesting novel treatments have been found in experimental models.

  13. SCIENTIFIC PRESENTATIONS of the 11. MEETING OF THE MANAGEMENT STEERING COMMITTEE OF THE RIKEN BNL COLLABORATION (RBRC SCIENTIFIC ARTICLE, VOLUME 11)

    International Nuclear Information System (INIS)

    Samios, N.P.

    2005-01-01

    The RIKEN BNL Research Center (RBRC) was established in April 1997 at Brookhaven National Laboratory. It is funded by the ''Rikagaku Kenkyusho,'' (RIKEN) The Institute of Physical and Chemical Research, of Japan. The Center is dedicated to the study of strong interactions, including hard QCD/spin physics, lattice QCD and RHIC (Relativistic Heavy Ion Collider) physics through nurturing of a new generation of young physicists. The agreement was extended in 2002 for another five year period. This 11th steering group meeting consisted of a series of reports on current activities and future perspectives. Presentation titles and authors included: 'RBRC operations and accomplishments' by Nicholas P. Samios, 'Theoretical physics at RIKEN-BNL Center: strong interactions and QCD' by Larry McLerran, 'RBRC experimental group and Wako base', by Hideto En'yo, 'The QCDOC project overview and status' by Norman H. Christ, 'RHIC spin physics' by Gerry Bunce, 'RHIC heavy ion progam' by Yasuyuki Akiba, 'RIKEN's current status and future plans' by Samuel Aronson, 'Procedure for proposing renewal of the collaboration agreement in 2007' by Chiharu Shimoyamada, and 'New direction of RPRC beyond JFY 2007' by Nicholas P. Samios

  14. Omics studies of citrus, grape and rosaceae fruit trees.

    Science.gov (United States)

    Shiratake, Katsuhiro; Suzuki, Mami

    2016-01-01

    Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted.

  15. Charged particle activation analysis at RIKEN. Past, present and future

    International Nuclear Information System (INIS)

    Nozaki, T.

    2008-01-01

    From 1960s to 1980s many groups in the world actively studied and utilized charged particle activation analysis (CPAA) mainly for absolute determination of B, C, N, and O in high-purity substances, particularly semiconductor materials. Here, after a short historical note on CPAA, works of the author's group mainly at RIKEN are outlined and then his opinion is shown about how to anticipate on the present shrinking of CPAA. (author)

  16. -Omic and Electronic Health Record Big Data Analytics for Precision Medicine.

    Science.gov (United States)

    Wu, Po-Yen; Cheng, Chih-Wen; Kaddi, Chanchala D; Venugopalan, Janani; Hoffman, Ryan; Wang, May D

    2017-02-01

    Rapid advances of high-throughput technologies and wide adoption of electronic health records (EHRs) have led to fast accumulation of -omic and EHR data. These voluminous complex data contain abundant information for precision medicine, and big data analytics can extract such knowledge to improve the quality of healthcare. In this paper, we present -omic and EHR data characteristics, associated challenges, and data analytics including data preprocessing, mining, and modeling. To demonstrate how big data analytics enables precision medicine, we provide two case studies, including identifying disease biomarkers from multi-omic data and incorporating -omic information into EHR. Big data analytics is able to address -omic and EHR data challenges for paradigm shift toward precision medicine. Big data analytics makes sense of -omic and EHR data to improve healthcare outcome. It has long lasting societal impact.

  17. NASA GeneLab Project: Bridging Space Radiation Omics with Ground Studies.

    Science.gov (United States)

    Beheshti, Afshin; Miller, Jack; Kidane, Yared; Berrios, Daniel; Gebre, Samrawit G; Costes, Sylvain V

    2018-04-13

    Accurate assessment of risks of long-term space missions is critical for human space exploration. It is essential to have a detailed understanding of the biological effects on humans living and working in deep space. Ionizing radiation from galactic cosmic rays (GCR) is a major health risk factor for astronauts on extended missions outside the protective effects of the Earth's magnetic field. Currently, there are gaps in our knowledge of the health risks associated with chronic low-dose, low-dose-rate ionizing radiation, specifically ions associated with high (H) atomic number (Z) and energy (E). The NASA GeneLab project ( https://genelab.nasa.gov/ ) aims to provide a detailed library of omics datasets associated with biological samples exposed to HZE. The GeneLab Data System (GLDS) includes datasets from both spaceflight and ground-based studies, a majority of which involve exposure to ionizing radiation. In addition to detailed information on radiation exposure for ground-based studies, GeneLab is adding detailed, curated dosimetry information for spaceflight experiments. GeneLab is the first comprehensive omics database for space-related research from which an investigator can generate hypotheses to direct future experiments, utilizing both ground and space biological radiation data. The GLDS is continually expanding as omics-related data are generated by the space life sciences community. Here we provide a brief summary of the space radiation-related data available at GeneLab.

  18. Journal of Biosciences | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    2007-08-06

    Aug 6, 2007 ... Author Affiliations. Pawan K Dhar1. Synthetic Genomics, Systems Biology Group, E209, RIKEN Genomic Sciences Centre, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan ...

  19. Making the Most of Omics for Symbiosis Research

    Science.gov (United States)

    Chaston, J.; Douglas, A.E.

    2012-01-01

    Omics, including genomics, proteomics and metabolomics, enable us to explain symbioses in terms of the underlying molecules and their interactions. The central task is to transform molecular catalogs of genes, metabolites etc. into a dynamic understanding of symbiosis function. We review four exemplars of omics studies that achieve this goal, through defined biological questions relating to metabolic integration and regulation of animal-microbial symbioses, the genetic autonomy of bacterial symbionts, and symbiotic protection of animal hosts from pathogens. As omic datasets become increasingly complex, computationally-sophisticated downstream analyses are essential to reveal interactions not evident to visual inspection of the data. We discuss two approaches, phylogenomics and transcriptional clustering, that can divide the primary output of omics studies – long lists of factors – into manageable subsets, and we describe how they have been applied to analyze large datasets and generate testable hypotheses. PMID:22983030

  20. A conceptual model for translating omic data into clinical action

    Directory of Open Access Journals (Sweden)

    Timothy M Herr

    2015-01-01

    Full Text Available Genomic, proteomic, epigenomic, and other "omic" data have the potential to enable precision medicine, also commonly referred to as personalized medicine. The volume and complexity of omic data are rapidly overwhelming human cognitive capacity, requiring innovative approaches to translate such data into patient care. Here, we outline a conceptual model for the application of omic data in the clinical context, called "the omic funnel." This model parallels the classic "Data, Information, Knowledge, Wisdom pyramid" and adds context for how to move between each successive layer. Its goal is to allow informaticians, researchers, and clinicians to approach the problem of translating omic data from bench to bedside, by using discrete steps with clearly defined needs. Such an approach can facilitate the development of modular and interoperable software that can bring precision medicine into widespread practice.

  1. -Omic and Electronic Health Records Big Data Analytics for Precision Medicine

    Science.gov (United States)

    Wu, Po-Yen; Cheng, Chih-Wen; Kaddi, Chanchala D.; Venugopalan, Janani; Hoffman, Ryan; Wang, May D.

    2017-01-01

    Objective Rapid advances of high-throughput technologies and wide adoption of electronic health records (EHRs) have led to fast accumulation of -omic and EHR data. These voluminous complex data contain abundant information for precision medicine, and big data analytics can extract such knowledge to improve the quality of health care. Methods In this article, we present -omic and EHR data characteristics, associated challenges, and data analytics including data pre-processing, mining, and modeling. Results To demonstrate how big data analytics enables precision medicine, we provide two case studies, including identifying disease biomarkers from multi-omic data and incorporating -omic information into EHR. Conclusion Big data analytics is able to address –omic and EHR data challenges for paradigm shift towards precision medicine. Significance Big data analytics makes sense of –omic and EHR data to improve healthcare outcome. It has long lasting societal impact. PMID:27740470

  2. Multi-omics approach to elucidate the gut microbiota activity: Metaproteomics and metagenomics connection.

    Science.gov (United States)

    Guirro, Maria; Costa, Andrea; Gual-Grau, Andreu; Mayneris-Perxachs, Jordi; Torrell, Helena; Herrero, Pol; Canela, Núria; Arola, Lluís

    2018-02-10

    Over the last few years, the application of high-throughput meta-omics methods has provided great progress in improving the knowledge of the gut ecosystem and linking its biodiversity to host health conditions, offering complementary support to classical microbiology. Gut microbiota plays a crucial role in relevant diseases such as obesity or cardiovascular disease (CVD), and its regulation is closely influenced by several factors, such as dietary composition. In fact, polyphenol-rich diets are the most palatable treatment to prevent hypertension associated with CVD, although the polyphenol-microbiota interactions have not been completely elucidated. For this reason, the aim of this study was to evaluate microbiota effect in obese rats supplemented by hesperidin, after being fed with cafeteria or standard diet, using a multi meta-omics approaches combining strategy of metagenomics and metaproteomics analysis. We reported that cafeteria diet induces obesity, resulting in changes in the microbiota composition, which are related to functional alterations at proteome level. In addition, hesperidin supplementation alters microbiota diversity and also proteins involved in important metabolic pathways. Overall, going deeper into strategies to integrate omics sciences is necessary to understand the complex relationships between the host, gut microbiota, and diet. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Present status of the Riken accelerator research facility (RARF)

    International Nuclear Information System (INIS)

    Kase, M.; Goto, A.; Kageyama, T.; Yokoyama, I.; Nagase, M.; Kohara, S.; Nakagawa, T.; Inabe, N.; Ikegami, K.; Kamigaito, O.; Kidera, M.; Fujita, J.; Yoneda, A.; Kobayashi, M.; Yano, Y.

    1999-01-01

    The K540-MeV RIKEN Ring Cyclotron (RRC) celebrated 10 years of successful beam operation in December 1996. The beam intensities have been increased over years to the present levels of about 500 pnA for 135 MeV/nucleon 12 C and of 2000 pnA for 24 MeV/nucleon 40 Ar. The variation of beam has now exceeded one hundred. These beams have been delivered to users in many fields. Improvements are being and will be made to upgrade the present machine to be matched as an injector to the program of the RI beam factory. (authors)

  4. Framework for the quality assurance of 'omics technologies considering GLP requirements.

    Science.gov (United States)

    Kauffmann, Hans-Martin; Kamp, Hennicke; Fuchs, Regine; Chorley, Brian N; Deferme, Lize; Ebbels, Timothy; Hackermüller, Jörg; Perdichizzi, Stefania; Poole, Alan; Sauer, Ursula G; Tollefsen, Knut E; Tralau, Tewes; Yauk, Carole; van Ravenzwaay, Ben

    2017-12-01

    'Omics technologies are gaining importance to support regulatory toxicity studies. Prerequisites for performing 'omics studies considering GLP principles were discussed at the European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) Workshop Applying 'omics technologies in Chemical Risk Assessment. A GLP environment comprises a standard operating procedure system, proper pre-planning and documentation, and inspections of independent quality assurance staff. To prevent uncontrolled data changes, the raw data obtained in the respective 'omics data recording systems have to be specifically defined. Further requirements include transparent and reproducible data processing steps, and safe data storage and archiving procedures. The software for data recording and processing should be validated, and data changes should be traceable or disabled. GLP-compliant quality assurance of 'omics technologies appears feasible for many GLP requirements. However, challenges include (i) defining, storing, and archiving the raw data; (ii) transparent descriptions of data processing steps; (iii) software validation; and (iv) ensuring complete reproducibility of final results with respect to raw data. Nevertheless, 'omics studies can be supported by quality measures (e.g., GLP principles) to ensure quality control, reproducibility and traceability of experiments. This enables regulators to use 'omics data in a fit-for-purpose context, which enhances their applicability for risk assessment. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. NASA GeneLab Project: Bridging Space Radiation Omics with Ground Studies

    Science.gov (United States)

    Beheshti, Afshin; Miller, Jack; Kidane, Yared H.; Berrios, Daniel; Gebre, Samrawit G.; Costes, Sylvain V.

    2018-01-01

    Accurate assessment of risk factors for long-term space missions is critical for human space exploration: therefore it is essential to have a detailed understanding of the biological effects on humans living and working in deep space. Ionizing radiation from Galactic Cosmic Rays (GCR) is one of the major risk factors factor that will impact health of astronauts on extended missions outside the protective effects of the Earth's magnetic field. Currently there are gaps in our knowledge of the health risks associated with chronic low dose, low dose rate ionizing radiation, specifically ions associated with high (H) atomic number (Z) and energy (E). The GeneLab project (genelab.nasa.gov) aims to provide a detailed library of Omics datasets associated with biological samples exposed to HZE. The GeneLab Data System (GLDS) currently includes datasets from both spaceflight and ground-based studies, a majority of which involve exposure to ionizing radiation. In addition to detailed information for ground-based studies, we are in the process of adding detailed, curated dosimetry information for spaceflight missions. GeneLab is the first comprehensive Omics database for space related research from which an investigator can generate hypotheses to direct future experiments utilizing both ground and space biological radiation data. In addition to previously acquired data, the GLDS is continually expanding as Omics related data are generated by the space life sciences community. Here we provide a brief summary of space radiation related data available at GeneLab.

  6. MADMAX - Management and analysis database for multiple ~omics experiments

    NARCIS (Netherlands)

    Lin, K.; Kools, H.J.; Groot, de P.J.; Gavai, A.K.; Basnet, R.K.; Bonnema, A.B.; Visser, R.G.F.; Leunissen, J.

    2011-01-01

    The rapid increase of ~omics datasets generated by microarray, mass spectrometry and next generation sequencing technologies requires an integrated platform that can combine results from different ~omics datasets to provide novel insights in the understanding of biological systems. MADMAX is

  7. Status report on RIKEN Ring Cyclotron

    International Nuclear Information System (INIS)

    Yano, Y.

    1988-01-01

    This paper gives a status report on RIKEN Ring Cyclotron (RRC), successfully commissioned on December 16, 1986. The routine operation of RRC began in April, 1987, and was made until March 1988. April and May were devoted to the machine studies, and beams were delivered to the experiments from the end of May. Seven kinds of ion species from carbon to copper were used for the nuclear physics and atomic physics experiments during these one-year runs. High quality beams with transverse emittances less than 10 mm mrad, energy spread of approximately 0.1% and pulse width less than 300 psec were extracted. Since the middle of March, 1988, RRC has been shut down for extending the beam transfer lines and installing the various experimental setups. Next experimental program will start in July, 1988. The initial operational status of RRC is described as well as the running construction program of the new injector, a K70 AVF cyclotron with an external ECR ion source

  8. FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data.

    Directory of Open Access Journals (Sweden)

    Takeru Uchiyama

    Full Text Available Exponential growth of high-throughput data and the increasing complexity of omics information have been making processing and interpreting biological data an extremely difficult and daunting task. Here we developed FuncTree (http://bioviz.tokyo/functree, a web-based application for analyzing and visualizing large-scale omics data, including but not limited to genomic, metagenomic, and transcriptomic data. FuncTree allows user to map their omics data onto the "Functional Tree map", a predefined circular dendrogram, which represents the hierarchical relationship of all known biological functions defined in the KEGG database. This novel visualization method allows user to overview the broad functionality of their data, thus allowing a more accurate and comprehensive understanding of the omics information. FuncTree provides extensive customization and calculation methods to not only allow user to directly map their omics data to identify the functionality of their data, but also to compute statistically enriched functions by comparing it to other predefined omics data. We have validated FuncTree's analysis and visualization capability by mapping pan-genomic data of three different types of bacterial genera, metagenomic data of the human gut, and transcriptomic data of two different types of human cell expression. All three mapping strongly confirms FuncTree's capability to analyze and visually represent key functional feature of the omics data. We believe that FuncTree's capability to conduct various functional calculations and visualizing the result into a holistic overview of biological function, would make it an integral analysis/visualization tool for extensive omics base research.

  9. Spectroscopy on neutron-rich nuclei at RIKEN. Present and future

    International Nuclear Information System (INIS)

    Sakurai, H.

    2003-01-01

    Recent studies on nuclear structure by using radioactive isotope beams available at the RIKEN projectile-fragment separator (RIPS) are introduced. Special emphasis is given to experiments selected from the recent programs that highlight studies at N=20-28; on the large deformation of 30 Ne and 34 Mg via the in-beam gamma spectroscopy, and on the particle stability of very neutron-rich nuclei, 34 Ne, 37 Na and 43 Si. The RI Beam Factory (RIBF) project is illustrated through review of such present research activities at RIPS. (author)

  10. Omics Data Complementarity Underlines Functional Cross-Communication in Yeast

    Directory of Open Access Journals (Sweden)

    Malod-Dognin Noël

    2017-06-01

    Full Text Available Mapping the complete functional layout of a cell and understanding the cross-talk between different processes are fundamental challenges. They elude us because of the incompleteness and noisiness of molecular data and because of the computational intractability of finding the exact answer. We perform a simple integration of three types of baker’s yeast omics data to elucidate the functional organization and lines of cross-functional communication. We examine protein–protein interaction (PPI, co-expression (COEX and genetic interaction (GI data, and explore their relationship with the gold standard of functional organization, the Gene Ontology (GO. We utilize a simple framework that identifies functional cross-communication lines in each of the three data types, in GO, and collectively in the integrated model of the three omics data types; we present each of them in our new Functional Organization Map (FOM model. We compare the FOMs of the three omics datasets with the FOM of GO and find that GI is in best agreement with GO, followed COEX and PPI. We integrate the three FOMs into a unified FOM and find that it is in better agreement with the FOM of GO than those of any omics dataset alone, demonstrating functional complementarity of different omics data.

  11. Omics Data Complementarity Underlines Functional Cross-Communication in Yeast.

    Science.gov (United States)

    Malod-Dognin, Noël; Pržulj, Nataša

    2017-06-10

    Mapping the complete functional layout of a cell and understanding the cross-talk between different processes are fundamental challenges. They elude us because of the incompleteness and noisiness of molecular data and because of the computational intractability of finding the exact answer. We perform a simple integration of three types of baker's yeast omics data to elucidate the functional organization and lines of cross-functional communication. We examine protein-protein interaction (PPI), co-expression (COEX) and genetic interaction (GI) data, and explore their relationship with the gold standard of functional organization, the Gene Ontology (GO). We utilize a simple framework that identifies functional cross-communication lines in each of the three data types, in GO, and collectively in the integrated model of the three omics data types; we present each of them in our new Functional Organization Map (FOM) model. We compare the FOMs of the three omics datasets with the FOM of GO and find that GI is in best agreement with GO, followed COEX and PPI. We integrate the three FOMs into a unified FOM and find that it is in better agreement with the FOM of GO than those of any omics dataset alone, demonstrating functional complementarity of different omics data.

  12. The nephrologist of tomorrow: towards a kidney-omic future.

    Science.gov (United States)

    Hanna, Mina H; Dalla Gassa, Alessandra; Mayer, Gert; Zaza, Gianluigi; Brophy, Patrick D; Gesualdo, Loreto; Pesce, Francesco

    2017-03-01

    Omics refers to the collective technologies used to explore the roles and relationships of the various types of molecules that make up the phenotype of an organism. Systems biology is a scientific discipline that endeavours to quantify all of the molecular elements of a biological system. Therefore, it reflects the knowledge acquired by omics in a meaningful manner by providing insights into functional pathways and regulatory networks underlying different diseases. The recent advances in biotechnological platforms and statistical tools to analyse such complex data have enabled scientists to connect the experimentally observed correlations to the underlying biochemical and pathological processes. We discuss in this review the current knowledge of different omics technologies in kidney diseases, specifically in the field of pediatric nephrology, including biomarker discovery, defining as yet unrecognized biologic therapeutic targets and linking omics to relevant standard indices and clinical outcomes. We also provide here a unique perspective on the field, taking advantage of the experience gained by the large-scale European research initiative called "Systems Biology towards Novel Chronic Kidney Disease Diagnosis and Treatment" (SysKid). Based on the integrative framework of Systems biology, SysKid demonstrated how omics are powerful yet complex tools to unravel the consequences of diabetes and hypertension on kidney function.

  13. QUARKONIUM PRODUCTION IN RELATIVISTIC NUCLEAR COLLISIONS. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP, VOLUME 12

    Energy Technology Data Exchange (ETDEWEB)

    KHARZEEV,D.

    1999-04-20

    The RIKEN-BNL Workshop on Quarkonium Production in Relativistic Nuclear Collisions was held September 28--October 2, 1998, at Brookhaven National Laboratory. The Workshop brought together about 50 invited participants from around the world and a number of Brookhaven physicists from both particle and nuclear physics communities.

  14. Quarkonium production in relativistic nuclear collisions. Proceedings of Riken BNL Research Center Workshop,Volume 12

    International Nuclear Information System (INIS)

    Kharzeev, D.

    1999-01-01

    The RIKEN-BNL Workshop on Quarkonium Production in Relativistic Nuclear Collisions was held September 28--October 2, 1998, at Brookhaven National Laboratory. The Workshop brought together about 50 invited participants from around the world and a number of Brookhaven physicists from both particle and nuclear physics communities

  15. Omics Advances in Ecotoxicology.

    Science.gov (United States)

    Zhang, Xiaowei; Xia, Pu; Wang, Pingping; Yang, Jianghu; Baird, Donald J

    2018-04-03

    Toxic substances in the environment generate adverse effects at all levels of biological organization from the molecular level to community and ecosystem. Given this complexity, it is not surprising that ecotoxicologists have struggled to address the full consequences of toxic substance release at ecosystem level, due to the limits of observational and experimental tools to reveal the changes in deep structure at different levels of organization. -Omics technologies, consisting of genomics and ecogenomics, have the power to reveal, in unprecedented detail, the cellular processes of an individual or biodiversity of a community in response to environmental change with high sample/observation throughput. This represents a historic opportunity to transform the way we study toxic substances in ecosystems, through direct linkage of ecological effects with the systems biology of organisms. Three recent examples of -omics advance in the assessment of toxic substances are explored here: (1) the use of functional genomics in the discovery of novel molecular mechanisms of toxicity of chemicals in the environment; (2) the development of laboratory pipelines of dose-dependent, reduced transcriptomics to support high-throughput chemical testing at the biological pathway level; and (3) the use of eDNA metabarcoding approaches for assessing chemical effects on biological communities in mesocosm experiments and through direct observation in field monitoring. -Omics advances in ecotoxicological studies not only generate new knowledge regarding mechanisms of toxicity and environmental effect, improving the relevance and immediacy of laboratory toxicological assessment, but can provide a wholly new paradigm for ecotoxicology by linking ecological models to mechanism-based, systems biology approaches.

  16. Are we closer to the vision? A proposed framework for incorporating omics into environmental assessments.

    Science.gov (United States)

    Martyniuk, Christopher J

    2018-04-01

    Environmental science has benefited a great deal from omics-based technologies. High-throughput toxicology has defined adverse outcome pathways (AOPs), prioritized chemicals of concern, and identified novel actions of environmental chemicals. While many of these approaches are conducted under rigorous laboratory conditions, a significant challenge has been the interpretation of omics data in "real-world" exposure scenarios. Clarity in the interpretation of these data limits their use in environmental monitoring programs. In recent years, one overarching objective of many has been to address fundamental questions concerning experimental design and the robustness of data collected under the broad umbrella of environmental genomics. These questions include: (1) the likelihood that molecular profiles return to a predefined baseline level following remediation efforts, (2) how reference site selection in an urban environment influences interpretation of omics data and (3) what is the most appropriate species to monitor in the environment from an omics point of view. In addition, inter-genomics studies have been conducted to assess transcriptome reproducibility in toxicology studies. One lesson learned from inter-genomics studies is that there are core molecular networks that can be identified by multiple laboratories using the same platform. This supports the idea that "omics-networks" defined a priori may be a viable approach moving forward for evaluating environmental impacts over time. Both spatial and temporal variability in ecosystem structure is expected to influence molecular responses to environmental stressors, and it is important to recognize how these variables, as well as individual factor (i.e. sex, age, maturation), may confound interpretation of network responses to chemicals. This mini-review synthesizes the progress made towards adopting these tools into environmental monitoring and identifies future challenges to be addressed, as we move into the next

  17. Production of intense beams of highly charged heavy ions from RIKEN 18 GHz ECRIS and liquid He free SC-ECRIS

    International Nuclear Information System (INIS)

    Nakagawa, T.; Kidera, M.; Kageyama, T.; Kase, M.; Yano, Y.; Higurashi, Y.; Kurita, T.; Imanaka, M.

    2001-01-01

    We have constructed the high performance ECRISs for RIKEN RI Beam factory project and successfully produced intense beams of highly charged heavy ions. RIKEN 18 GHz ECRIS can especially produce intense beams of medium charge states of heavy ions (1.3 mA of Ar 8+ , 200 eμA of Xe 20+ ) by applying the various techniques, e.g., Al cylinder method, biased electrode method, optimization of the plasma electrode position. Very recently, we successfully produced intense beams of highly charged heavy ions (10 eμA of Xe 30+ , 1 eμA of Xe 36+ ) from the Liquid He free SC-ECRIS with operational frequency of 14 GHz

  18. Using omics and integrated multi-omics approaches to guide probiotic selection to mitigate chytridiomycosis and other emerging infectious diseases

    Directory of Open Access Journals (Sweden)

    Eria Alaide Rebollar

    2016-02-01

    Full Text Available Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called omics, are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools and in silico models that link bacterial community structure with bacterial defensive function can allow the identification of species involved in pathogen inhibition. We recommend using 16S rRNA gene amplicon sequencing and methods such as indicator species analysis, the K-S Measure, and co-occurrence networks to identify bacteria that are associated with pathogen resistance in field surveys and experimental trials. In addition to 16S amplicon sequencing, we recommend approaches that give insight into symbiont function such as shotgun metagenomics, metatranscriptomics or metabolomics to maximize the probability of finding effective probiotic candidates, which can then be isolated in culture and tested in persistence and clinical trials. An effective mitigation strategy to ameliorate chytridiomycosis and other emerging infectious diseases is necessary; the advancement of omic methods and the integration of multiple omic data provide a promising avenue toward conservation of imperiled species.

  19. Clinical multi-omics strategies for the effective cancer management.

    Science.gov (United States)

    Yoo, Byong Chul; Kim, Kyung-Hee; Woo, Sang Myung; Myung, Jae Kyung

    2017-08-15

    Cancer is a global health issue as a multi-factorial complex disease, and early detection and novel therapeutic strategies are required for more effective cancer management. With the development of systemic analytical -omics strategies, the therapeutic approach and study of the molecular mechanisms of carcinogenesis and cancer progression have moved from hypothesis-driven targeted investigations to data-driven untargeted investigations focusing on the integrated diagnosis, treatment, and prevention of cancer in individual patients. Predictive, preventive, and personalized medicine (PPPM) is a promising new approach to reduce the burden of cancer and facilitate more accurate prognosis, diagnosis, as well as effective treatment. Here we review the fundamentals of, and new developments in, -omics technologies, together with the key role of a variety of practical -omics strategies in PPPM for cancer treatment and diagnosis. In this review, a comprehensive and critical overview of the systematic strategy for predictive, preventive, and personalized medicine (PPPM) for cancer disease was described in a view of cancer prognostic prediction, diagnostics, and prevention as well as cancer therapy and drug responses. We have discussed multi-dimensional data obtained from various resources and integration of multisciplinary -omics strategies with computational method which could contribute the more effective PPPM for cancer. This review has provided the novel insights of the current applications of each and combined -omics technologies, which showed their powerful potential for the establishment of PPPM for cancer. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Omicseq: a web-based search engine for exploring omics datasets

    Science.gov (United States)

    Sun, Xiaobo; Pittard, William S.; Xu, Tianlei; Chen, Li; Zwick, Michael E.; Jiang, Xiaoqian; Wang, Fusheng

    2017-01-01

    Abstract The development and application of high-throughput genomics technologies has resulted in massive quantities of diverse omics data that continue to accumulate rapidly. These rich datasets offer unprecedented and exciting opportunities to address long standing questions in biomedical research. However, our ability to explore and query the content of diverse omics data is very limited. Existing dataset search tools rely almost exclusively on the metadata. A text-based query for gene name(s) does not work well on datasets wherein the vast majority of their content is numeric. To overcome this barrier, we have developed Omicseq, a novel web-based platform that facilitates the easy interrogation of omics datasets holistically to improve ‘findability’ of relevant data. The core component of Omicseq is trackRank, a novel algorithm for ranking omics datasets that fully uses the numerical content of the dataset to determine relevance to the query entity. The Omicseq system is supported by a scalable and elastic, NoSQL database that hosts a large collection of processed omics datasets. In the front end, a simple, web-based interface allows users to enter queries and instantly receive search results as a list of ranked datasets deemed to be the most relevant. Omicseq is freely available at http://www.omicseq.org. PMID:28402462

  1. Stepping into the omics era: Opportunities and challenges for biomaterials science and engineering.

    Science.gov (United States)

    Groen, Nathalie; Guvendiren, Murat; Rabitz, Herschel; Welsh, William J; Kohn, Joachim; de Boer, Jan

    2016-04-01

    The research paradigm in biomaterials science and engineering is evolving from using low-throughput and iterative experimental designs towards high-throughput experimental designs for materials optimization and the evaluation of materials properties. Computational science plays an important role in this transition. With the emergence of the omics approach in the biomaterials field, referred to as materiomics, high-throughput approaches hold the promise of tackling the complexity of materials and understanding correlations between material properties and their effects on complex biological systems. The intrinsic complexity of biological systems is an important factor that is often oversimplified when characterizing biological responses to materials and establishing property-activity relationships. Indeed, in vitro tests designed to predict in vivo performance of a given biomaterial are largely lacking as we are not able to capture the biological complexity of whole tissues in an in vitro model. In this opinion paper, we explain how we reached our opinion that converging genomics and materiomics into a new field would enable a significant acceleration of the development of new and improved medical devices. The use of computational modeling to correlate high-throughput gene expression profiling with high throughput combinatorial material design strategies would add power to the analysis of biological effects induced by material properties. We believe that this extra layer of complexity on top of high-throughput material experimentation is necessary to tackle the biological complexity and further advance the biomaterials field. In this opinion paper, we postulate that converging genomics and materiomics into a new field would enable a significant acceleration of the development of new and improved medical devices. The use of computational modeling to correlate high-throughput gene expression profiling with high throughput combinatorial material design strategies would

  2. Annual report of the Institute of Physical and Chemical Research, for fiscal 1999

    International Nuclear Information System (INIS)

    2000-01-01

    The research activities in the Institute of Physical and Chemical Research (RIKEN) for the fiscal year 1999 were briefly described in this report. In addition, the research papers published in the year from the laboratories in RIKEN Wako Main Campus, RIKEN Tsukuba Research Center of Life Science and RIKEN Harima Institute were presented. Moreover, ten special research projects for basic science are now progressing on the following themes: photosynthetic science (artificial photosynthesis and the mechanism of photosynthesis), biodesign research (cellular function system, membranous function system), coherent science research (coherent control for free electron, quantum processing, structural control and coherent molecular interaction), research on multi-bioprobes (development of multi-functional bioactive compounds), research on essential reaction (stereo-control and energy control), atomic-scale sciengineering (phase 2 study), MR science research (phase 2 study), slow quantum beam production of ultra slow highly charged ions and ecomolecular science research (material conversion and biological/chemical conversion for environmental compounds). The research activities of RIKEN Brain Science Institute were also outlined and RIKEN Genomic Sciences Center were also outlined. In the year, RIKEN symposium was held 38 times by various laboratories. Here, the themes of these symposia were listed as well as those of international symposia sponsored by RIKEN Institute. (M.N.)

  3. Integration, warehousing, and analysis strategies of Omics data.

    Science.gov (United States)

    Gedela, Srinubabu

    2011-01-01

    "-Omics" is a current suffix for numerous types of large-scale biological data generation procedures, which naturally demand the development of novel algorithms for data storage and analysis. With next generation genome sequencing burgeoning, it is pivotal to decipher a coding site on the genome, a gene's function, and information on transcripts next to the pure availability of sequence information. To explore a genome and downstream molecular processes, we need umpteen results at the various levels of cellular organization by utilizing different experimental designs, data analysis strategies and methodologies. Here comes the need for controlled vocabularies and data integration to annotate, store, and update the flow of experimental data. This chapter explores key methodologies to merge Omics data by semantic data carriers, discusses controlled vocabularies as eXtensible Markup Languages (XML), and provides practical guidance, databases, and software links supporting the integration of Omics data.

  4. Single cell analysis: the new frontier in 'Omics'

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Daojing; Bodovitz, Steven

    2010-01-14

    Cellular heterogeneity arising from stochastic expression of genes, proteins, and metabolites is a fundamental principle of cell biology, but single cell analysis has been beyond the capabilities of 'Omics' technologies. This is rapidly changing with the recent examples of single cell genomics, transcriptomics, proteomics, and metabolomics. The rate of change is expected to accelerate owing to emerging technologies that range from micro/nanofluidics to microfabricated interfaces for mass spectrometry to third- and fourth-generation automated DNA sequencers. As described in this review, single cell analysis is the new frontier in Omics, and single cell Omics has the potential to transform systems biology through new discoveries derived from cellular heterogeneity.

  5. The Use of Omic Technologies Applied to Traditional Chinese Medicine Research

    Directory of Open Access Journals (Sweden)

    Dalinda Isabel Sánchez-Vidaña

    2017-01-01

    Full Text Available Natural products represent one of the most important reservoirs of structural and chemical diversity for the generation of leads in the drug development process. A growing number of researchers have shown interest in the development of drugs based on Chinese herbs. In this review, the use and potential of omic technologies as powerful tools in the modernization of traditional Chinese medicine are discussed. The analytical combination from each omic approach is crucial for understanding the working mechanisms of cells, tissues, organs, and organisms as well as the mechanisms of disease. Gradually, omic approaches have been introduced in every stage of the drug development process to generate high-quality Chinese medicine-based drugs. Finally, the future picture of the use of omic technologies is a promising tool and arena for further improvement in the modernization of traditional Chinese medicine.

  6. News in livestock research - use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals.

    Science.gov (United States)

    Deusch, Simon; Tilocca, Bruno; Camarinha-Silva, Amélia; Seifert, Jana

    2015-01-01

    Technical progress in the field of next-generation sequencing, mass spectrometry and bioinformatics facilitates the study of highly complex biological samples such as taxonomic and functional characterization of microbial communities that virtually colonize all present ecological niches. Compared to the structural information obtained by metagenomic analyses, metaproteomic approaches provide, in addition, functional data about the investigated microbiota. In general, integration of the main Omics-technologies (genomics, transcriptomics, proteomics and metabolomics) in live science promises highly detailed information about the specific research object and helps to understand molecular changes in response to internal and external environmental factors. The microbial communities settled in the mammalian gastrointestinal tract are essential for the host metabolism and have a major impact on its physiology and health. The microbiotas of livestock like chicken, pig and ruminants are becoming a focus of interest for veterinaries, animal nutritionists and microbiologists. While pig is more often used as an animal model for human-related studies, the rumen microbiota harbors a diversity of enzymes converting complex carbohydrates into monomers which bears high potential for biotechnological applications. This review will provide a general overview about the recent Omics-based research of the microbiota in livestock including its major findings. Differences concerning the results of pre-Omics-approaches in livestock as well as the perspectives of this relatively new Omics-platform will be highlighted.

  7. Omicseq: a web-based search engine for exploring omics datasets.

    Science.gov (United States)

    Sun, Xiaobo; Pittard, William S; Xu, Tianlei; Chen, Li; Zwick, Michael E; Jiang, Xiaoqian; Wang, Fusheng; Qin, Zhaohui S

    2017-07-03

    The development and application of high-throughput genomics technologies has resulted in massive quantities of diverse omics data that continue to accumulate rapidly. These rich datasets offer unprecedented and exciting opportunities to address long standing questions in biomedical research. However, our ability to explore and query the content of diverse omics data is very limited. Existing dataset search tools rely almost exclusively on the metadata. A text-based query for gene name(s) does not work well on datasets wherein the vast majority of their content is numeric. To overcome this barrier, we have developed Omicseq, a novel web-based platform that facilitates the easy interrogation of omics datasets holistically to improve 'findability' of relevant data. The core component of Omicseq is trackRank, a novel algorithm for ranking omics datasets that fully uses the numerical content of the dataset to determine relevance to the query entity. The Omicseq system is supported by a scalable and elastic, NoSQL database that hosts a large collection of processed omics datasets. In the front end, a simple, web-based interface allows users to enter queries and instantly receive search results as a list of ranked datasets deemed to be the most relevant. Omicseq is freely available at http://www.omicseq.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Omics methods for probing the mode of action of natural and synthetic phytotoxins.

    Science.gov (United States)

    Duke, Stephen O; Bajsa, Joanna; Pan, Zhiqiang

    2013-02-01

    For a little over a decade, omics methods (transcriptomics, proteomics, metabolomics, and physionomics) have been used to discover and probe the mode of action of both synthetic and natural phytotoxins. For mode of action discovery, the strategy for each of these approaches is to generate an omics profile for phytotoxins with known molecular targets and to compare this library of responses to the responses of compounds with unknown modes of action. Using more than one omics approach enhances the probability of success. Generally, compounds with the same mode of action generate similar responses with a particular omics method. Stress and detoxification responses to phytotoxins can be much clearer than effects directly related to the target site. Clues to new modes of action must be validated with in vitro enzyme effects or genetic approaches. Thus far, the only new phytotoxin target site discovered with omics approaches (metabolomics and physionomics) is that of cinmethylin and structurally related 5-benzyloxymethyl-1,2-isoxazolines. These omics approaches pointed to tyrosine amino-transferase as the target, which was verified by enzyme assays and genetic methods. In addition to being a useful tool of mode of action discovery, omics methods provide detailed information on genetic and biochemical impacts of phytotoxins. Such information can be useful in understanding the full impact of natural phytotoxins in both agricultural and natural ecosystems.

  9. RIKEN accelerator progress report, vol. 18

    International Nuclear Information System (INIS)

    Ambe, S.; Awaya, Y.; Gono, Y.; Inamura, T.; Kamitsubo, H.; Kitayama, S.; Odera, M.; Watanabe, T.; Yagi, E.

    1985-06-01

    The collaborative research using the 160 cm cyclotron and the variable frequency, heavy ion linear accelerator (RILAC) has been extensively performed in this year. In addition, an electrostatic accelerator (TANDETRON) of IMV and an ion implanter of 250 kV were dedicated to the collaborative research. During the past one year, the cyclotron was in good condition, and a new gas feed system was developed as the cyclotron ion source. The operation of the RILAC in a full 17 - 45 MHz range was realized. The TANDETRON has been steadily operated. The nuclear spectroscopy and reaction mechanism for heavy ion collision were studied. Instrument development was continued for the purpose of building the new experimental equipment for SSC. Experiments were carried out on the beam foil spectroscopy and atomic collision measuring ultra-violet ray, x-ray, Auger electrons and recoil ions. Moessbauer spectroscopy and perturbed angular correlation studies were continued. The creep and helium bubble formation in fusion reactor materials by bombarding with alpha particles and protons were studied in cooperation with the National Research Institute for Metals. The construction of the Riken Ring Cyclotron progressed. (Kako, I.)

  10. Machine Learning Approaches to Increasing Value of Spaceflight Omics Databases

    Science.gov (United States)

    Gentry, Diana

    2017-01-01

    The number of spaceflight bioscience mission opportunities is too small to allow all relevant biological and environmental parameters to be experimentally identified. Simulated spaceflight experiments in ground-based facilities (GBFs), such as clinostats, are each suitable only for particular investigations -- a rotating-wall vessel may be 'simulated microgravity' for cell differentiation (hours), but not DNA repair (seconds) -- and introduce confounding stimuli, such as motor vibration and fluid shear effects. This uncertainty over which biological mechanisms respond to a given form of simulated space radiation or gravity, as well as its side effects, limits our ability to baseline spaceflight data and validate mission science. Machine learning techniques autonomously identify relevant and interdependent factors in a data set given the set of desired metrics to be evaluated: to automatically identify related studies, compare data from related studies, or determine linkages between types of data in the same study. System-of-systems (SoS) machine learning models have the ability to deal with both sparse and heterogeneous data, such as that provided by the small and diverse number of space biosciences flight missions; however, they require appropriate user-defined metrics for any given data set. Although machine learning in bioinformatics is rapidly expanding, the need to combine spaceflight/GBF mission parameters with omics data is unique. This work characterizes the basic requirements for implementing the SoS approach through the System Map (SM) technique, a composite of a dynamic Bayesian network and Gaussian mixture model, in real-world repositories such as the GeneLab Data System and Life Sciences Data Archive. The three primary steps are metadata management for experimental description using open-source ontologies, defining similarity and consistency metrics, and generating testing and validation data sets. Such approaches to spaceflight and GBF omics data may

  11. Perturbative QCD as a probe of hadron structure: Volume 2. Proceedings of RIKEN BNL Research Center workshop

    International Nuclear Information System (INIS)

    1997-01-01

    The workshop brought together about thirty invited participants from around the world, and an almost equal number of Brookhaven users and staff, to discuss recent developments and future prospects for hadronic strong interaction studies at high energy, particularly relating to the RHIC project at Brookhaven. RIKEN and Brookhaven have long traditions in and commitments to the study of the strong interactions, and the advent of the RHIC collider will open new opportunities both for relativistic heavy ion and polarized proton-proton studies. Activities at the RIKEN BNL Research Center are intended to focus on physics opportunities stimulated by this new facility. Thus, one of the purposes of the center is to provide a forum where workers in the field can gather to share and develop their ideas in a stimulating environment. The purpose of the workshop was both to delineate theoretical problems and stimulate collaborations to address them. The workshop focused primarily, but not exclusively, on spin and small-x physics

  12. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP, VOLUME 65, RHIC SPIN COLLABORATION MEETINGS XXVII, XXVIII, and XXX

    International Nuclear Information System (INIS)

    OGAWA, A.

    2004-01-01

    The RIKEN BNL Research Center (RSRC) was established in April 1997 at Brookhaven National Laboratory. It is funded by the 'Rikagaku Kenkyusho' (RIKEN, The Institute of Physical and Chemical Research) of Japan. The Center is dedicated to the study of strong interactions, including spin physics, lattice QCD, and RHIC physics through the nurturing of a new generation of young physicists. The RBRC has both a theory and experimental component. At present the theoretical group has 4 Fellows and 3 Research Associates as well as 11 RHIC Physics/University Fellows (academic year 2003-2004). To date there are approximately 30 graduates from the program of which 13 have attained tenure positions at major institutions worldwide. The experimental group is smaller and has 2 Fellows and 3 RHIC Physics/University Fellows and 3 Research Associates, and historically 6 individuals have attained permanent positions. Beginning in 2001 a new RIKEN Spin Program (RSP) category was implemented at RBRC. These appointments are joint positions of RBRC and RIKEN and include the following positions in theory and experiment: RSP Researchers, RSP Research Associates, and Young Researchers, who are mentored by senior RBRC Scientists, A number of RIKEN Jr. Research Associates and Visiting Scientists also contribute to the physics program at the Center. RBRC has an active workshop program on strong interaction physics with each workshop focused on a specific physics problem. Each workshop speaker is encouraged to select a few of the most important transparencies from his or her presentation, accompanied by a page of explanation. This material is collected at the end of the workshop by the organizer to form proceedings, which can therefore be available within a short time. To date there are sixty nine proceedings volumes available. The construction of a 0.6 teraflops parallel processor, dedicated to lattice QCD, begun at the Center on February 19, 1998, was completed on August 28, 1998 and is still

  13. Omics methods for probing the mode of action of natural phytotoxins

    Science.gov (United States)

    For a little over a decade, omics methods (transcriptomics, proteomics, metabolomics, and physionomics) have been used to discover and probe the mode of action of both synthetic and natural phytotoxins. For mode of action discovery, the strategy for each of these approaches is to generate an omics...

  14. GeneLab: Multi-Omics Investigation of Rodent Research-1 Bio-Banked Tissues

    Science.gov (United States)

    Lai, San-Huei; Boyko, Valery; Chakravarty, Kaushik; Chen, Rick; Dueck, Sandra; Berrios, Daniel C.; Fogle, Homer; Marcu, Oana; Timucin, Linda; Reinsch, Sigrid; hide

    2016-01-01

    NASAs Rodent Research (RR) project is playing a critical role in advancing biomedical research on the physiological effects of space environments. Due to the limited resources for conducting biological experiments aboard the International Space Station (ISS), it is imperative to use crew time efficiently while maximizing high-quality science return. NASAs GeneLab project has as its primary objectives to 1) further increase the value of these experiments using a multi-omics, systems biology-based approach, and 2) disseminate these data without restrictions to the scientific community. The current investigation assessed viability of RNA, DNA, and protein extracted from archived RR-1 tissue samples for epigenomic, transcriptomic, and proteomic assays. During the first RR spaceflight experiment, a variety of tissue types were harvested from subjects, snap-frozen or RNAlater-preserved, and then stored at least a year at -80OC after return to Earth. They were then prioritized for this investigation based on likelihood of significant scientific value for spaceflight research. All tissues were made available to GeneLab through the bio-specimen sharing program managed by the Ames Life Science Data Archive and included mouse adrenal glands, quadriceps, gastrocnemius, tibialis anterior, extensor digitorum longus, soleus, eye, and kidney. We report here protocols for and results of these tissue extractions, and thus, the feasibility and value of these kinds of omics analyses. In addition to providing additional opportunities for investigation of spaceflight effects on the mouse transcriptome and proteome in new kinds of tissues, our results may also be of value to program managers for the prioritization of ISS crew time for rodent research activities. Support from the NASA Space Life and Physical Sciences Division and the International Space Station Program is gratefully acknowledged.

  15. Allele Frequency - JSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available nd 39 SNPs are assayed in three (POP_*) and two (RIKEN_japanese_*) panels, respectively. Derived from Flat f... assay (JBIC-allele and RIKEN_japanese_*), TaqMan assay (RIKEN-allele) or direct sequencing / allelic discri...unteers under informed consent RIKEN_japanese_normal_weight - 711 unrelated japanese normal weight volunteer...s ( body mass index RIKEN_japanese_obese - 796 unrelated japanese obese patients

  16. Annual report of the Institute of Physical and Chemical Research, for fiscal 1998

    International Nuclear Information System (INIS)

    1999-01-01

    This annual report describes the abstracts of researches and oral presentations and papers reported as the results for fiscal 1998 in each laboratory of RIKEN (the Institute of Physical and Chemical Research). Moreover, the themes of special project funding for basic science, grant research, contract research, industrial properties, research subjects of special postdoctoral researchers and junior research associate and technology research subjects of technology research fellow are inserted. The abstract of researches, oral presentations and publications reported by Frontier Research Program, Brain Science Institute, Riken and Riken Genomic Science Center are contained. Riken Symposia and Symposia Sponsored by Riken are explained. (S.Y.)

  17. A generic Transcriptomics Reporting Framework (TRF) for 'omics data processing and analysis.

    Science.gov (United States)

    Gant, Timothy W; Sauer, Ursula G; Zhang, Shu-Dong; Chorley, Brian N; Hackermüller, Jörg; Perdichizzi, Stefania; Tollefsen, Knut E; van Ravenzwaay, Ben; Yauk, Carole; Tong, Weida; Poole, Alan

    2017-12-01

    A generic Transcriptomics Reporting Framework (TRF) is presented that lists parameters that should be reported in 'omics studies used in a regulatory context. The TRF encompasses the processes from transcriptome profiling from data generation to a processed list of differentially expressed genes (DEGs) ready for interpretation. Included within the TRF is a reference baseline analysis (RBA) that encompasses raw data selection; data normalisation; recognition of outliers; and statistical analysis. The TRF itself does not dictate the methodology for data processing, but deals with what should be reported. Its principles are also applicable to sequencing data and other 'omics. In contrast, the RBA specifies a simple data processing and analysis methodology that is designed to provide a comparison point for other approaches and is exemplified here by a case study. By providing transparency on the steps applied during 'omics data processing and analysis, the TRF will increase confidence processing of 'omics data, and regulatory use. Applicability of the TRF is ensured by its simplicity and generality. The TRF can be applied to all types of regulatory 'omics studies, and it can be executed using different commonly available software tools. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

  18. Implications of the recent D-T μCF experiments at RIKEN-RAL and near-future directions

    International Nuclear Information System (INIS)

    Nagamine, K.; Matsuzaki, T.; Ishida, K.; Nakamura, S.N.; Kawamura, N.

    1999-01-01

    The paper describes physics implications obtained through the recent experimental results on D-T μCF at RIKEN-RAL. Smaller sticking and larger cycling rates in solid/liquid D-T mixture than the theoretical predictions were observed, suggesting needs of further theoretical understandings. Some possible future directions in D-T μCF experiments are also described

  19. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP: VOLUME 69 RBRC SCIENTIFIC REVIEW COMMITTEE MEETING

    International Nuclear Information System (INIS)

    SAMIOS, N.P.

    2005-01-01

    The RIKEN BNL Research Center (RSRC) was established in April 1997 at Brookhaven National Laboratory. It is funded by the 'Rikagaku Kenkyusho' (RIKEN, The Institute of Physical and Chemical Research) of Japan. The Center is dedicated to the study of strong interactions, including spin physics, lattice QCD, and RHIC physics through the nurturing of a new generation of young physicists. The RBRC has both a theory and experimental component. At present the theoretical group has 4 Fellows and 3 Research Associates as well as 11 RHIC Physics/University Fellows (academic year 2003-2004). To date there are approximately 30 graduates from the program of which 13 have attained tenure positions at major institutions worldwide. The experimental group is smaller and has 2 Fellows and 3 RHIC Physics/University Fellows and 3 Research Associates, and historically 6 individuals have attained permanent positions. Beginning in 2001 a new RIKEN Spin Program (RSP) category was implemented at RBRC. These appointments are joint positions of RBRC and RIKEN and include the following positions in theory and experiment: RSP Researchers, RSP Research Associates, and Young Researchers, who are mentored by senior RBRC Scientists, A number of RIKEN Jr. Research Associates and Visiting Scientists also contribute to the physics program at the Center. RBRC has an active workshop program on strong interaction physics with each workshop focused on a specific physics problem. Each workshop speaker is encouraged to select a few of the most important transparencies from his or her presentation, accompanied by a page of explanation. This material is collected at the end of the workshop by the organizer to form proceedings, which can therefore be available within a short time. To date there are sixty nine proceedings volumes available. The construction of a 0.6 teraflops parallel processor, dedicated to lattice QCD, begun at the Center on February 19, 1998, was completed on August 28, 1998 and is still

  20. Integrated omics analysis of specialized metabolism in medicinal plants.

    Science.gov (United States)

    Rai, Amit; Saito, Kazuki; Yamazaki, Mami

    2017-05-01

    Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to explore the biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. However, recent advances in high-throughput large-scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant-based medicinal metabolites. The reduced cost of generating omics datasets and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several bioactive metabolites of plant origin. These discoveries have inspired synthetic biology approaches to develop microbial systems to produce bioactive metabolites originating from plants, an alternative sustainable source of medicinally important chemicals. Since the demand for medicinal compounds are increasing with the world's population, understanding the complete biosynthesis of specialized metabolites becomes important to identify or develop reliable sources in the future. Here, we review the contributions of major omics approaches and their integration to our understanding of the biosynthetic pathways of bioactive metabolites. We briefly discuss different approaches for integrating omics datasets to extract biologically relevant knowledge and the application of omics datasets in the construction and reconstruction of metabolic models. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  1. A retrospective likelihood approach for efficient integration of multiple omics factors in case-control association studies.

    Science.gov (United States)

    Balliu, Brunilda; Tsonaka, Roula; Boehringer, Stefan; Houwing-Duistermaat, Jeanine

    2015-03-01

    Integrative omics, the joint analysis of outcome and multiple types of omics data, such as genomics, epigenomics, and transcriptomics data, constitute a promising approach for powerful and biologically relevant association studies. These studies often employ a case-control design, and often include nonomics covariates, such as age and gender, that may modify the underlying omics risk factors. An open question is how to best integrate multiple omics and nonomics information to maximize statistical power in case-control studies that ascertain individuals based on the phenotype. Recent work on integrative omics have used prospective approaches, modeling case-control status conditional on omics, and nonomics risk factors. Compared to univariate approaches, jointly analyzing multiple risk factors with a prospective approach increases power in nonascertained cohorts. However, these prospective approaches often lose power in case-control studies. In this article, we propose a novel statistical method for integrating multiple omics and nonomics factors in case-control association studies. Our method is based on a retrospective likelihood function that models the joint distribution of omics and nonomics factors conditional on case-control status. The new method provides accurate control of Type I error rate and has increased efficiency over prospective approaches in both simulated and real data. © 2015 Wiley Periodicals, Inc.

  2. Omics Methods for Probing the Mode of Action of Natural and Synthetic Phytotoxins

    OpenAIRE

    Duke, Stephen O.; Bajsa, Joanna; Pan, Zhiqiang

    2013-01-01

    For a little over a decade, omics methods (transcriptomics, proteomics, metabolomics, and physionomics) have been used to discover and probe the mode of action of both synthetic and natural phytotoxins. For mode of action discovery, the strategy for each of these approaches is to generate an omics profile for phytotoxins with known molecular targets and to compare this library of responses to the responses of compounds with unknown modes of action. Using more than one omics approach enhances ...

  3. Multi-omics analysis provides insight to the Ignicoccus hospitalis-Nanoarchaeum equitans association.

    Science.gov (United States)

    Rawle, Rachel A; Hamerly, Timothy; Tripet, Brian P; Giannone, Richard J; Wurch, Louie; Hettich, Robert L; Podar, Mircea; Copié, Valerie; Bothner, Brian

    2017-09-01

    Studies of interspecies interactions are inherently difficult due to the complex mechanisms which enable these relationships. A model system for studying interspecies interactions is the marine hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans. Recent independently-conducted 'omics' analyses have generated insights into the molecular factors modulating this association. However, significant questions remain about the nature of the interactions between these archaea. We jointly analyzed multiple levels of omics datasets obtained from published, independent transcriptomics, proteomics, and metabolomics analyses. DAVID identified functionally-related groups enriched when I. hospitalis is grown alone or in co-culture with N. equitans. Enriched molecular pathways were subsequently visualized using interaction maps generated using STRING. Key findings of our multi-level omics analysis indicated that I. hospitalis provides precursors to N. equitans for energy metabolism. Analysis indicated an overall reduction in diversity of metabolic precursors in the I. hospitalis-N. equitans co-culture, which has been connected to the differential use of ribosomal subunits and was previously unnoticed. We also identified differences in precursors linked to amino acid metabolism, NADH metabolism, and carbon fixation, providing new insights into the metabolic adaptions of I. hospitalis enabling the growth of N. equitans. This multi-omics analysis builds upon previously identified cellular patterns while offering new insights into mechanisms that enable the I. hospitalis-N. equitans association. Our study applies statistical and visualization techniques to a mixed-source omics dataset to yield a more global insight into a complex system, that was not readily discernable from separate omics studies. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. The role of the clinician in the multi-omics era: are you ready?

    Science.gov (United States)

    van Karnebeek, Clara D M; Wortmann, Saskia B; Tarailo-Graovac, Maja; Langeveld, Mirjam; Ferreira, Carlos R; van de Kamp, Jiddeke M; Hollak, Carla E; Wasserman, Wyeth W; Waterham, Hans R; Wevers, Ron A; Haack, Tobias B; Wanders, Ronald J A; Boycott, Kym M

    2018-01-23

    Since Garrod's first description of alkaptonuria in 1902, and newborn screening for phenylketonuria introduced in the 1960s, P4 medicine (preventive, predictive, personalized, and participatory) has been a reality for the clinician serving patients with inherited metabolic diseases. The era of high-throughput technologies promises to accelerate its scale dramatically. Genomics, transcriptomics, epigenomics, proteomics, glycomics, metabolomics, and lipidomics offer an amazing opportunity for holistic investigation and contextual pathophysiologic understanding of inherited metabolic diseases for precise diagnosis and tailored treatment. While each of the -omics technologies is important to systems biology, some are more mature than others. Exome sequencing is emerging as a reimbursed test in clinics around the world, and untargeted metabolomics has the potential to serve as a single biochemical testing platform. The challenge lies in the integration and cautious interpretation of these big data, with translation into clinically meaningful information and/or action for our patients. A daunting but exciting task for the clinician; we provide clinical cases to illustrate the importance of his/her role as the connector between physicians, laboratory experts and researchers in the basic, computer, and clinical sciences. Open collaborations, data sharing, functional assays, and model organisms play a key role in the validation of -omics discoveries. Having all the right expertise at the table when discussing the diagnostic approach and individualized management plan according to the information yielded by -omics investigations (e.g., actionable mutations, novel therapeutic interventions), is the stepping stone of P4 medicine. Patient participation and the adjustment of the medical team's plan to his/her and the family's wishes most certainly is the capstone. Are you ready?

  5. Multi-omics facilitated variable selection in Cox-regression model for cancer prognosis prediction.

    Science.gov (United States)

    Liu, Cong; Wang, Xujun; Genchev, Georgi Z; Lu, Hui

    2017-07-15

    New developments in high-throughput genomic technologies have enabled the measurement of diverse types of omics biomarkers in a cost-efficient and clinically-feasible manner. Developing computational methods and tools for analysis and translation of such genomic data into clinically-relevant information is an ongoing and active area of investigation. For example, several studies have utilized an unsupervised learning framework to cluster patients by integrating omics data. Despite such recent advances, predicting cancer prognosis using integrated omics biomarkers remains a challenge. There is also a shortage of computational tools for predicting cancer prognosis by using supervised learning methods. The current standard approach is to fit a Cox regression model by concatenating the different types of omics data in a linear manner, while penalty could be added for feature selection. A more powerful approach, however, would be to incorporate data by considering relationships among omics datatypes. Here we developed two methods: a SKI-Cox method and a wLASSO-Cox method to incorporate the association among different types of omics data. Both methods fit the Cox proportional hazards model and predict a risk score based on mRNA expression profiles. SKI-Cox borrows the information generated by these additional types of omics data to guide variable selection, while wLASSO-Cox incorporates this information as a penalty factor during model fitting. We show that SKI-Cox and wLASSO-Cox models select more true variables than a LASSO-Cox model in simulation studies. We assess the performance of SKI-Cox and wLASSO-Cox using TCGA glioblastoma multiforme and lung adenocarcinoma data. In each case, mRNA expression, methylation, and copy number variation data are integrated to predict the overall survival time of cancer patients. Our methods achieve better performance in predicting patients' survival in glioblastoma and lung adenocarcinoma. Copyright © 2017. Published by Elsevier

  6. MONGKIE: an integrated tool for network analysis and visualization for multi-omics data.

    Science.gov (United States)

    Jang, Yeongjun; Yu, Namhee; Seo, Jihae; Kim, Sun; Lee, Sanghyuk

    2016-03-18

    Network-based integrative analysis is a powerful technique for extracting biological insights from multilayered omics data such as somatic mutations, copy number variations, and gene expression data. However, integrated analysis of multi-omics data is quite complicated and can hardly be done in an automated way. Thus, a powerful interactive visual mining tool supporting diverse analysis algorithms for identification of driver genes and regulatory modules is much needed. Here, we present a software platform that integrates network visualization with omics data analysis tools seamlessly. The visualization unit supports various options for displaying multi-omics data as well as unique network models for describing sophisticated biological networks such as complex biomolecular reactions. In addition, we implemented diverse in-house algorithms for network analysis including network clustering and over-representation analysis. Novel functions include facile definition and optimized visualization of subgroups, comparison of a series of data sets in an identical network by data-to-visual mapping and subsequent overlaying function, and management of custom interaction networks. Utility of MONGKIE for network-based visual data mining of multi-omics data was demonstrated by analysis of the TCGA glioblastoma data. MONGKIE was developed in Java based on the NetBeans plugin architecture, thus being OS-independent with intrinsic support of module extension by third-party developers. We believe that MONGKIE would be a valuable addition to network analysis software by supporting many unique features and visualization options, especially for analysing multi-omics data sets in cancer and other diseases. .

  7. Leveraging Algal Omics to Reveal Potential Targets for Augmenting TAG Accumulation

    Energy Technology Data Exchange (ETDEWEB)

    Guarnieri, Michael T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Pienkos, Philip T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Arora, Neha [Indian Institute of Technology Roorkee; Pruthi, Vikas [Indian Institute of Technology Roorkee; Poluri, Krishna Mohan [Indian Institute of Technology Roorkee

    2018-04-18

    Ongoing global efforts to commercialize microalgal biofuels have expedited the use of multi-omics techniques to gain insights into lipid biosynthetic pathways. Functional genomics analyses have recently been employed to complement existing sequence-level omics studies, shedding light on the dynamics of lipid synthesis and its interplay with other cellular metabolic pathways, thus revealing possible targets for metabolic engineering. Here, we review the current status of algal omics studies to reveal potential targets to augment TAG accumulation in various microalgae. This review specifically aims to examine and catalog systems level data related to stress-induced TAG accumulation in oleaginous microalgae and inform future metabolic engineering strategies to develop strains with enhanced bioproductivity, which could pave a path for sustainable green energy.

  8. Report from the Third Annual Symposium of the RIKEN-Max Planck Joint Research Center for Systems Chemical Biology.

    Science.gov (United States)

    Brunschweiger, Andreas

    2014-08-15

    The third Annual Symposium of the RIKEN-Max Planck Joint Research Center for Systems Chemical Biology was held at Ringberg castle, May 21-24, 2014. At this meeting 45 scientists from Japan and Germany presented the latest results from their research spanning a broad range of topics in chemical biology and glycobiology.

  9. ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding.

    Science.gov (United States)

    Guhlin, Joseph; Silverstein, Kevin A T; Zhou, Peng; Tiffin, Peter; Young, Nevin D

    2017-08-10

    Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotated datasets available on the web with few ways to link them to in-lab datasets. With so many research groups generating their own data, the ability to relate it to the larger genomic and comparative genomic context is becoming increasingly crucial to make full use of the data. The Omics Database Generator (ODG) allows users to create customized databases that utilize published genomics data integrated with experimental data which can be queried using a flexible graph database. When provided with omics and experimental data, ODG will create a comparative, multi-dimensional graph database. ODG can import definitions and annotations from other sources such as InterProScan, the Gene Ontology, ENZYME, UniPathway, and others. This annotation data can be especially useful for studying new or understudied species for which transcripts have only been predicted, and rapidly give additional layers of annotation to predicted genes. In better studied species, ODG can perform syntenic annotation translations or rapidly identify characteristics of a set of genes or nucleotide locations, such as hits from an association study. ODG provides a web-based user-interface for configuring the data import and for querying the database. Queries can also be run from the command-line and the database can be queried directly through programming language hooks available for most languages. ODG supports most common genomic formats as well as generic, easy to use tab-separated value format for user-provided annotations. ODG is a user-friendly database generation and query tool that adapts to the supplied data to produce a comparative genomic database or multi-layered annotation database. ODG provides rapid comparative genomic annotation and is therefore particularly useful for non-model or

  10. A fully Bayesian latent variable model for integrative clustering analysis of multi-type omics data.

    Science.gov (United States)

    Mo, Qianxing; Shen, Ronglai; Guo, Cui; Vannucci, Marina; Chan, Keith S; Hilsenbeck, Susan G

    2018-01-01

    Identification of clinically relevant tumor subtypes and omics signatures is an important task in cancer translational research for precision medicine. Large-scale genomic profiling studies such as The Cancer Genome Atlas (TCGA) Research Network have generated vast amounts of genomic, transcriptomic, epigenomic, and proteomic data. While these studies have provided great resources for researchers to discover clinically relevant tumor subtypes and driver molecular alterations, there are few computationally efficient methods and tools for integrative clustering analysis of these multi-type omics data. Therefore, the aim of this article is to develop a fully Bayesian latent variable method (called iClusterBayes) that can jointly model omics data of continuous and discrete data types for identification of tumor subtypes and relevant omics features. Specifically, the proposed method uses a few latent variables to capture the inherent structure of multiple omics data sets to achieve joint dimension reduction. As a result, the tumor samples can be clustered in the latent variable space and relevant omics features that drive the sample clustering are identified through Bayesian variable selection. This method significantly improve on the existing integrative clustering method iClusterPlus in terms of statistical inference and computational speed. By analyzing TCGA and simulated data sets, we demonstrate the excellent performance of the proposed method in revealing clinically meaningful tumor subtypes and driver omics features. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Fluxomics - connecting 'omics analysis and phenotypes.

    Science.gov (United States)

    Winter, Gal; Krömer, Jens O

    2013-07-01

    In our modern 'omics era, metabolic flux analysis (fluxomics) represents the physiological counterpart of its siblings transcriptomics, proteomics and metabolomics. Fluxomics integrates in vivo measurements of metabolic fluxes with stoichiometric network models to allow the determination of absolute flux through large networks of the central carbon metabolism. There are many approaches to implement fluxomics including flux balance analysis (FBA), (13) C fluxomics and (13) C-constrained FBA as well as many experimental settings for flux measurement including dynamic, stationary and semi-stationary. Here we outline the principles of the different approaches and their relative advantages. We demonstrate the unique contribution of flux analysis for phenotype elucidation using a thoroughly studied metabolic reaction as a case study, the microbial aerobic/anaerobic shift, highlighting the importance of flux analysis as a single layer of data as well as interlaced in multi-omics studies. © 2012 John Wiley & Sons Ltd and Society for Applied Microbiology.

  12. Role of omics techniques in the toxicity testing of nanoparticles

    Directory of Open Access Journals (Sweden)

    Eleonore Fröhlich

    2017-11-01

    Full Text Available Abstract Nanotechnology is regarded as a key technology of the twenty-first century. Despite the many advantages of nanotechnology it is also known that engineered nanoparticles (NPs may cause adverse health effects in humans. Reports on toxic effects of NPs relay mainly on conventional (phenotypic testing but studies of changes in epigenome, transcriptome, proteome, and metabolome induced by NPs have also been performed. NPs most relevant for human exposure in consumer, health and food products are metal, metal oxide and carbon-based NPs. They were also studied quite frequently with omics technologies and an overview of the study results can serve to answer the question if screening for established targets of nanotoxicity (e.g. cell death, proliferation, oxidative stress, and inflammation is sufficient or if omics techniques are needed to reveal new targets. Regulated pathways identified by omics techniques were confirmed by phenotypic assays performed in the same study and comparison of particle types and cells by the same group indicated a more cell/organ-specific than particle specific regulation pattern. Between different studies moderate overlap of the regulated pathways was observed and cell-specific regulation is less obvious. The lack of standardization in particle exposure, in omics technologies, difficulties to translate mechanistic data to phenotypes and comparison with human in vivo data currently limit the use of these technologies in the prediction of toxic effects by NPs.

  13. Results of RIKEN superconducting electron cyclotron resonance ion source with 28 GHz.

    Science.gov (United States)

    Higurashi, Y; Ohnishi, J; Nakagawa, T; Haba, H; Tamura, M; Aihara, T; Fujimaki, M; Komiyama, M; Uchiyama, A; Kamigaito, O

    2012-02-01

    We measured the beam intensity of highly charged heavy ions and x-ray heat load for RIKEN superconducting electron cyclotron resonance ion source with 28 GHz microwaves under the various conditions. The beam intensity of Xe(20+) became maximum at B(min) ∼ 0.65 T, which was ∼65% of the magnetic field strength of electron cyclotron resonance (B(ECR)) for 28 GHz microwaves. We observed that the heat load of x-ray increased with decreasing gas pressure and field gradient at resonance zone. It seems that the beam intensity of highly charged heavy ions with 28 GHz is higher than that with 18 GHz at same RF power.

  14. Renal injury in neonates: use of "omics" for developing precision medicine in neonatology.

    Science.gov (United States)

    Joshi, Mandar S; Montgomery, Kelsey A; Giannone, Peter J; Bauer, John A; Hanna, Mina H

    2017-01-01

    Preterm birth is associated with increased risks of morbidity and mortality along with increased healthcare costs. Advances in medicine have enhanced survival for preterm infants but the overall incidence of major morbidities has changed very little. Abnormal renal development is an important consequence of premature birth. Acute kidney injury (AKI) in the neonatal period is multifactorial and may increase lifetime risk of chronic kidney disease.Traditional biomarkers in newborns suffer from considerable confounders, limiting their use for early identification of AKI. There is a need to develop novel biomarkers that can identify, in real time, the evolution of renal dysfunction in an early diagnostic, monitoring and prognostic fashion. Use of "omics", particularly metabolomics, may provide valuable information regarding functional pathways underlying AKI and prediction of clinical outcomes.The emerging knowledge generated by the application of "omics" (genomics, proteomics, metabolomics) in neonatology provides new insights that can help to identify markers of early diagnosis, disease progression, and identify new therapeutic targets. Additionally, omics will have major implications in the field of personalized healthcare in the future. Here, we will review the current knowledge of different omics technologies in neonatal-perinatal medicine including biomarker discovery, defining as yet unrecognized biologic therapeutic targets, and linking of omics to relevant standard indices and long-term outcomes.

  15. Proceedings of the 5th workshop of 'quantum complex phenomena, -superconductivity, magnetism and phonon-' under the NIMS-RIKEN-JAEA cooperative research program on quantum beam science and technology

    International Nuclear Information System (INIS)

    Shamoto, Shin-ichi; Kodama, Katsuaki

    2012-08-01

    The 5th workshop of the NIMS-RIKEN-JAEA Cooperative Research Program 'Quantum Complex Phenomena, -Superconductivity, Magnetism and Phonon-' was held on January 23-24, 2012 at KKR Hakone Miyanoshita. This workshop is aimed to reveal the mechanism of quantum complex phenomena for the developments of next generation functional materials on the basis of 'Joint Research Agreement for the Pioneering R and D with Quantum Beam Technology' concluded by NIMS, RIKEN and JAEA on December 20, 2006. The neutron facilities in Tokai, i.e., the research reactor JRR-3 and the proton accelerator J-PARC (Japan Proton Accelerator Research Complex), were damaged by the Tohoku-Kanto earthquake on March 11, 2011. J-PARC members' devoted efforts for the recovery made it possible to successfully produce neutron beam in the midnight of January 24, just after this workshop. Also at JRR-3 all the repair works of the reactor facilities and buildings have been completed by the end of the fiscal year 2011. Yet, the safety analysis report is to be submitted and after its positive review by the national regulatory authority, the JRR-3 can undergo the regular periodic inspection to resume its operation. Under this circumstance, characteristic technologies, instruments, and distinguished researches of each institute about 'Superconductivity, Magnetism and Phonon' are introduced and discussed in addition to research outcomes of this Joint Research Agreement including a future prospect of this research area. This report includes abstracts and materials of the presentations in the workshop. (author)

  16. RIKEN RI Beam Factory and recent research activities

    International Nuclear Information System (INIS)

    Ueno, H.

    2014-01-01

    RIKEN has started the operation of the new facility for the Radioactive-Isotope Beam Factory (RIBF) project since 2006. In this project, intense primary beams are delivered at the energy E/A = 345 MeV over the whole range of the atomic number under the cyclotron-cascade acceleration scheme. The current, stability and sustainability in beam delivery have been increased significantly by recent improvement of the accelerator system. A high-current primary beam is then used to produce radioactive-isotope beams at the world's highest current utilizing the superconducting in-flight RI separator BigRIPS. Following the BigRIPS separator, several large-scale experimental key devices have been / will be installed, in order to fully capitalize the RIBF project. Owing to these progresses, nuclear structure information on far-unstable nuclei, which cannot be obtained by conventional technology, are now capable of being measured. Furthermore, in addition to such BigRIPS-related devices, other original experimental devices have been also newly installed at the lower energy experimental sites. Unique research opportunities are now available at the RIBF facility. (author)

  17. Serial-omics characterization of equine urine.

    Directory of Open Access Journals (Sweden)

    Min Yuan

    Full Text Available Horse urine is easily collected and contains molecules readily measurable using mass spectrometry that can be used as biomarkers representative of health, disease or drug tampering. This study aimed at analyzing microliter levels of horse urine to purify, identify and quantify proteins, polar metabolites and non-polar lipids. Urine from a healthy 12 year old quarter horse mare on a diet of grass hay and vitamin/mineral supplements with limited pasture access was collected for serial-omics characterization. The urine was treated with methyl tert-butyl ether (MTBE and methanol to partition into three distinct layers for protein, non-polar lipid and polar metabolite content from a single liquid-liquid extraction and was repeated two times. Each layer was analyzed by high performance liquid chromatography-high resolution tandem mass spectrometry (LC-MS/MS to obtain protein sequence and relative protein levels as well as identify and quantify small polar metabolites and lipids. The results show 46 urine proteins, many related to normal kidney function, structural and circulatory proteins as well as 474 small polar metabolites but only 10 lipid molecules. Metabolites were mostly related to urea cycle and ammonia recycling as well as amino acid related pathways, plant diet specific molecules, etc. The few lipids represented triglycerides and phospholipids. These data show a complete mass spectrometry based-omics characterization of equine urine from a single 333 μL mid-stream urine aliquot. These omics data help serve as a baseline for healthy mare urine composition and the analyses can be used to monitor disease progression, health status, monitor drug use, etc.

  18. Integrative Analysis of Omics Big Data.

    Science.gov (United States)

    Yu, Xiang-Tian; Zeng, Tao

    2018-01-01

    The diversity and huge omics data take biology and biomedicine research and application into a big data era, just like that popular in human society a decade ago. They are opening a new challenge from horizontal data ensemble (e.g., the similar types of data collected from different labs or companies) to vertical data ensemble (e.g., the different types of data collected for a group of person with match information), which requires the integrative analysis in biology and biomedicine and also asks for emergent development of data integration to address the great changes from previous population-guided to newly individual-guided investigations.Data integration is an effective concept to solve the complex problem or understand the complicate system. Several benchmark studies have revealed the heterogeneity and trade-off that existed in the analysis of omics data. Integrative analysis can combine and investigate many datasets in a cost-effective reproducible way. Current integration approaches on biological data have two modes: one is "bottom-up integration" mode with follow-up manual integration, and the other one is "top-down integration" mode with follow-up in silico integration.This paper will firstly summarize the combinatory analysis approaches to give candidate protocol on biological experiment design for effectively integrative study on genomics and then survey the data fusion approaches to give helpful instruction on computational model development for biological significance detection, which have also provided newly data resources and analysis tools to support the precision medicine dependent on the big biomedical data. Finally, the problems and future directions are highlighted for integrative analysis of omics big data.

  19. Accelerators in RIKEN from 1910's to the present (Part Three)

    International Nuclear Information System (INIS)

    Kamitsubo, Hiromichi

    2006-01-01

    The nuclear experiment laboratory was established by H. Nagaoka, Y. Nishina and S. Nishikawa in 1931. A cyclotron using Pullsen arc generator was built at the start. The effects of neutron on mouse and paraffin were researched by the cyclotron. This small cyclotron realized stabilization of the magnetic field at first in the world. Outline of small cyclotron and large cyclotron, and details of building of two cyclotrons are described. The large cyclotron was completed in 1943, and nuclear experiments using accelerated deuteron were begun. However, the large and small cyclotrons were destructed by USA army depended on the finish of the Second World War in 1945. After that, the heavy ion cyclotron was constructed by RIKEN in 1962. (S.Y.)

  20. Recent progress in the use of 'omics technologies in brassicaceous vegetables

    Directory of Open Access Journals (Sweden)

    Katja eWitzel

    2015-04-01

    Full Text Available Continuing advances in 'omics methodologies and instrumentation is enhancing the under-standing of how plants cope with the dynamic nature of their growing environment. 'Omics platforms have been only recently extended to cover horticultural crop species. Many of the most widely cultivated vegetable crops belong to the genus Brassica: these include plants grown for their root (turnip, rutabaga/swede, their swollen stem base (kohlrabi, their leaves (cabbage, kale, pak choi and their inflorescence (cauliflower, broccoli.Characterization at the genome, transcript, protein and metabolite levels has illustrated the complexity of the cellular response to a whole series of environmental stresses, including nutrient deficiency, pathogen attack, heavy metal toxicity, cold acclimation, and excessive and sub-optimal irradiation. This review covers recent applications of 'omics technologies to the brassicaceous vegetables, and discusses future scenarios in achieving improvements in crop end-use quality.

  1. SCIENTIFIC PRESENTATION. 7TH MEETING OF THE MANAGEMENT STEERING COMMITTEE OF THE RIKEN BNL COLLABORATION.

    Energy Technology Data Exchange (ETDEWEB)

    Lee, T.D.

    2001-02-13

    The RIKEN BNL Research Center (RBRC) was established in April 1997 at Brookhaven National Laboratory. It is funded by the ''Rikagaku Kenkysho,'' (RIKEN) The Institute of Physical and Chemical Research, of Japan. The Center is dedicated to the study of strong interactions, including hard QCD/spin physics, lattice QCD and RHIC (Relativistic Heavy Ion Collider) physics through nurturing of a new generation of young physicists. The Director of RBRC is Professor T. D. Lee. The first years were dedicated to the establishment of a theory group. This has essentially been completed consisting of Fellows, Postdocs, and RHIC Physics/University Fellows, with an active group of consultants. The center also organizes an extensive series of workshops on specific topics in strong interactions with an accompanying series of published proceedings. In addition, a 0.6 teraflop parallel processor computer has been constructed and operational since August 1998. It was awarded the Supercomputer 1998 Gordon Bell Prize for price performance. An active experimental group centered around the spin physics program at RHIC has subsequently also been established at RBRC. It presently consists of five Fellows, one Postdoc and several scientific collaborators with more appointments being expected in the near future. Members and participants of RBRC on occasion will develop articles such as this one, in the nature of a status report or a general review.

  2. SCIENTIFIC PRESENTATION. 7TH MEETING OF THE MANAGEMENT STEERING COMMITTEE OF THE RIKEN BNL COLLABORATION.

    Energy Technology Data Exchange (ETDEWEB)

    LEE,T.D.

    2001-02-13

    The RIKEN BNL Research Center (RBRC) was established in April 1997 at Brookhaven National Laboratory. It is funded by the ''Rikagaku Kenkysho,'' (RIKEN) The Institute of Physical and Chemical Research, of Japan. The Center is dedicated to the study of strong 'interactions, including hard QCD/spin physics, lattice QCD and RHIC (Relativistic Heavy Ion Collider) physics through nurturing of a new generation of young physicists. The Director of RBRC is Professor T. D. Lee. The first years were dedicated to the establishment of a theory group. This has essentially been completed consisting of Fellows, Postdocs, and RHIC Physics/University Fellows, with an active group of consultants. The center also organizes an extensive series of workshops on specific topics in strong interactions with an accompanying series of published proceedings. In addition, a 0.6 teraflop parallel processor computer has been constructed and operational since August 1998. It was awarded the Supercomputer 1998 Gordon Bell Prize for price performance. An active experimental group centered around the spin physics program at RHIC has subsequently also been established at RBRC. It presently consists of five Fellows, one Postdoc and several scientific collaborators with more appointments being expected in the near future. Members and participants of RBRC on occasion will develop articles such as this one, in the nature of a status report or a general review.

  3. Scientific presentation. 7th meeting of the management steering committee of the RIKEN BNL Collaboration

    International Nuclear Information System (INIS)

    Lee, T.D.

    2001-01-01

    The RIKEN BNL Research Center (RBRC) was established in April 1997 at Brookhaven National Laboratory. It is funded by the ''Rikagaku Kenkysho,'' (RIKEN) The Institute of Physical and Chemical Research, of Japan. The Center is dedicated to the study of strong interactions, including hard QCD/spin physics, lattice QCD and RHIC (Relativistic Heavy Ion Collider) physics through nurturing of a new generation of young physicists. The Director of RBRC is Professor T. D. Lee. The first years were dedicated to the establishment of a theory group. This has essentially been completed consisting of Fellows, Postdocs, and RHIC Physics/University Fellows, with an active group of consultants. The center also organizes an extensive series of workshops on specific topics in strong interactions with an accompanying series of published proceedings. In addition, a 0.6 teraflop parallel processor computer has been constructed and operational since August 1998. It was awarded the Supercomputer 1998 Gordon Bell Prize for price performance. An active experimental group centered around the spin physics program at RHIC has subsequently also been established at RBRC. It presently consists of five Fellows, one Postdoc and several scientific collaborators with more appointments being expected in the near future. Members and participants of RBRC on occasion will develop articles such as this one, in the nature of a status report or a general review

  4. Visual comparative omics of fungi for plant biomass deconstruction

    Directory of Open Access Journals (Sweden)

    Shingo Miyauchi

    2016-08-01

    Full Text Available Wood-decay fungi are able to decompose plant cell wall components such as cellulose, hemicelluloses and lignin. Such fungal capabilities may be exploited for the enhancement of directed enzymatic degradation of recalcitrant plant biomass. The comparative analysis of wood-decay fungi using a multi-omics approach gives not only new insights into the strategies for decomposing complex plant materials but also basic knowledge for the design of combinations of enzymes for biotechnological applications. We have developed an analytical workflow, Applied Biomass Conversion Design for Efficient Fungal Green Technology (ABCDEFGT, to simplify the analysis and interpretation of transcriptomic and secretomic data. The ABCDEFGT workflow is primarily constructed of self-organizing maps for grouping genes with similar transcription patterns and an overlay with secreted proteins. The ABCDEFGT workflow produces simple graphic outputs of genome-wide transcriptomes and secretomes. It enables visual inspection without a priori of the omics data, facilitating discoveries of co-regulated genes and proteins. Genome-wide omics landscapes were built with the newly sequenced fungal species Pycnoporus coccineus, Pycnoporus sanguineus, and Pycnoporus cinnabarinus grown on various carbon sources. Integration of the post-genomic data showed a global overlap, confirming the pertinence of the genome-wide approach to study the fungal biological responses to the carbon sources. Our method was compared to a recently-developed clustering method in order to assess the biological relevance of the method and ease of interpretation. Our approach provided a better biological representation of fungal behaviors. The genome-wide multi-omics strategy allowed us to determine the potential synergy of enzymes participating in the decomposition of cellulose, hemicellulose and lignin such as Lytic Polysaccharide Monooxygenases (LPMO, modular enzymes associated with a cellulose binding module

  5. Integrating Multi-omic features exploiting Chromosome Conformation Capture data

    Directory of Open Access Journals (Sweden)

    Ivan eMerelli

    2015-02-01

    Full Text Available The representation, integration and interpretation of omic data is a complex task, in particular considering the huge amount of information that is daily produced in molecular biology laboratories all around the world. The reason is that sequencing data regarding expression profiles, methylation patterns, and chromatin domains is difficult to harmonize in a systems biology view, since genome browsers only allow coordinate-based representations, discarding functional clusters created by the spatial conformation of the DNA in the nucleus. In this context, recent progresses in high throughput molecular biology techniques and bioinformatics have provided insights into chromatin interactions on a larger scale and offer a formidable support for the interpretation of multi-omic data. In particular, a novel sequencing technique called Chromosome Conformation Capture (3C allows the analysis of the chromosome organization in the cell’s natural state. While performed genome wide, this technique is usually called Hi-C. Inspired by service applications such as Google Maps, we developed NuChart, an R package that integrates Hi-C data to describe the chromosomal neighbourhood starting from the information about gene positions, with the possibility of mapping on the achieved graphs genomic features such as methylation patterns and histone modifications, along with expression profiles. In this paper we show the importance of the NuChart application for the integration of multi-omic data in a systems biology fashion, with particular interest in cytogenetic applications of these techniques. Moreover, we demonstrate how the integration of multi-omic data can provide useful information in understanding why genes are in certain specific positions inside the nucleus and how epigenetic patterns correlate with their expression.

  6. Bernard Lerer: recipient of the 2014 inaugural Werner Kalow Responsible Innovation Prize in Global Omics and Personalized Medicine (Pacific Rim Association for Clinical Pharmacogenetics).

    Science.gov (United States)

    Ozdemir, Vural; Endrenyi, Laszlo; Aynacıoğlu, Sükrü; Bragazzi, Nicola Luigi; Dandara, Collet; Dove, Edward S; Ferguson, Lynnette R; Geraci, Christy Jo; Hafen, Ernst; Kesim, Belgin Eroğlu; Kolker, Eugene; Lee, Edmund J D; Llerena, Adrian; Nacak, Muradiye; Shimoda, Kazutaka; Someya, Toshiyuki; Srivastava, Sanjeeva; Tomlinson, Brian; Vayena, Effy; Warnich, Louise; Yaşar, Umit

    2014-04-01

    This article announces the recipient of the 2014 inaugural Werner Kalow Responsible Innovation Prize in Global Omics and Personalized Medicine by the Pacific Rim Association for Clinical Pharmacogenetics (PRACP): Bernard Lerer, professor of psychiatry and director of the Biological Psychiatry Laboratory, Hadassah-Hebrew University Medical Center, Jerusalem, Israel. The Werner Kalow Responsible Innovation Prize is given to an exceptional interdisciplinary scholar who has made highly innovative and enduring contributions to global omics science and personalized medicine, with both vertical and horizontal (transdisciplinary) impacts. The prize is established in memory of a beloved colleague, mentor, and friend, the late Professor Werner Kalow, who cultivated the idea and practice of pharmacogenetics in modern therapeutics commencing in the 1950s. PRACP, the prize's sponsor, is one of the longest standing learned societies in the Asia-Pacific region, and was founded by Kalow and colleagues more than two decades ago in the then-emerging field of pharmacogenetics. In announcing this inaugural prize and its winner, we seek to highlight the works of prize winner, Professor Lerer. Additionally, we contextualize the significance of the prize by recalling the life and works of Professor Kalow and providing a brief socio-technical history of the rise of pharmacogenetics and personalized medicine as a veritable form of 21(st) century scientific practice. The article also fills a void in previous social science analyses of pharmacogenetics, by bringing to the fore the works of Kalow from 1995 to 2008, when he presciently noted the rise of yet another field of postgenomics inquiry--pharmacoepigenetics--that railed against genetic determinism and underscored the temporal and spatial plasticity of genetic components of drug response, with invention of the repeated drug administration (RDA) method that estimates the dynamic heritabilities of drug response. The prize goes a long way

  7. The human gut microbiome and its dysfunctions through the meta-omics prism.

    Science.gov (United States)

    Mondot, Stanislas; Lepage, Patricia

    2016-05-01

    The microorganisms inhabiting the human gut are abundant (10(14) cells) and diverse (approximately 500 species per individual). It is now acknowledged that the microbiota has coevolved with its host to achieve a symbiotic relationship, leading to physiological homeostasis. The gut microbiota ensures vital functions, such as food digestibility, maturation of the host immune system, and protection against pathogens. Over the last few decades, the gut microbiota has also been associated with numerous diseases, such as inflammatory bowel disease, irritable bowel syndrome, obesity, and metabolic diseases. In most of these pathologies, a microbial dysbiosis has been found, indicating shifts in the taxonomic composition of the gut microbiota and changes in its functionality. Our understanding of the influence of the gut microbiota on human health is still growing. Working with microorganisms residing in the gut is challenging since most of them are anaerobic and a vast majority (approximately 75%) are uncultivable to date. Recently, a wide range of new approaches (meta-omics) has been developed to bypass the uncultivability and reveal the intricate mechanisms that sustain gut microbial homeostasis. After a brief description of these approaches (metagenomics, metatranscriptomics, metaproteomics, and metabolomics), this review will discuss the importance of considering the gut microbiome as a structured ecosystem and the use of meta-omics to decipher dysfunctions of the gut microbiome in diseases. © 2016 New York Academy of Sciences.

  8. Application of omics data in regulatory toxicology: report of an international BfR expert workshop.

    Science.gov (United States)

    Marx-Stoelting, P; Braeuning, A; Buhrke, T; Lampen, A; Niemann, L; Oelgeschlaeger, M; Rieke, S; Schmidt, F; Heise, T; Pfeil, R; Solecki, R

    2015-11-01

    Advances in omics techniques and molecular toxicology are necessary to provide new perspectives for regulatory toxicology. By the application of modern molecular techniques, more mechanistic information should be gained to support standard toxicity studies and to contribute to a reduction and refinement of animal experiments required for certain regulatory purposes. The relevance and applicability of data obtained by omics methods to regulatory purposes such as grouping of chemicals, mode of action analysis or classification and labelling needs further improvement, defined validation and cautious expert judgment. Based on the results of an international expert workshop organized 2014 by the Federal Institute for Risk Assessment in Berlin, this paper is aimed to provide a critical overview of the regulatory relevance and reliability of omics methods, basic requirements on data quality and validation, as well as regulatory criteria to decide which effects observed by omics methods should be considered adverse or non-adverse. As a way forward, it was concluded that the inclusion of omics data can facilitate a more flexible approach for regulatory risk assessment and may help to reduce or refine animal testing.

  9. MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics.

    Science.gov (United States)

    Zhai, Peng; Yang, Longshu; Guo, Xiao; Wang, Zhe; Guo, Jiangtao; Wang, Xiaoqi; Zhu, Huaiqiu

    2017-10-02

    During the past decade, the development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled the characterization of microbial communities through metagenomics, metatranscriptomics, metaproteomics and metabolomics data. To reveal the diversity of microbial communities and interactions between living conditions and microbes, it is necessary to introduce comparative analysis based upon integration of all four types of data mentioned above. Comparative meta-omics, especially comparative metageomics, has been established as a routine process to highlight the significant differences in taxon composition and functional gene abundance among microbiota samples. Meanwhile, biologists are increasingly concerning about the correlations between meta-omics features and environmental factors, which may further decipher the adaptation strategy of a microbial community. We developed a graphical comprehensive analysis software named MetaComp comprising a series of statistical analysis approaches with visualized results for metagenomics and other meta-omics data comparison. This software is capable to read files generated by a variety of upstream programs. After data loading, analyses such as multivariate statistics, hypothesis testing of two-sample, multi-sample as well as two-group sample and a novel function-regression analysis of environmental factors are offered. Here, regression analysis regards meta-omic features as independent variable and environmental factors as dependent variables. Moreover, MetaComp is capable to automatically choose an appropriate two-group sample test based upon the traits of input abundance profiles. We further evaluate the performance of its choice, and exhibit applications for metagenomics, metaproteomics and metabolomics samples. MetaComp, an integrative software capable for applying to all meta-omics data, originally distills the influence of living environment on microbial community by regression analysis

  10. Deciphering functional diversification within the lichen microbiota by meta-omics.

    Science.gov (United States)

    Cernava, Tomislav; Erlacher, Armin; Aschenbrenner, Ines Aline; Krug, Lisa; Lassek, Christian; Riedel, Katharina; Grube, Martin; Berg, Gabriele

    2017-07-19

    Recent evidence of specific bacterial communities extended the traditional concept of fungal-algal lichen symbioses by a further organismal kingdom. Although functional roles were already assigned to dominant members of the highly diversified microbiota, a substantial fraction of the ubiquitous colonizers remained unexplored. We employed a multi-omics approach to further characterize functional guilds in an unconventional model system. The general community structure of the lichen-associated microbiota was shown to be highly similar irrespective of the employed omics approach. Five highly abundant bacterial orders-Sphingomonadales, Rhodospirillales, Myxococcales, Chthoniobacterales, and Sphingobacteriales-harbor functions that are of substantial importance for the holobiome. Identified functions range from the provision of vitamins and cofactors to the degradation of phenolic compounds like phenylpropanoid, xylenols, and cresols. Functions that facilitate the persistence of Lobaria pulmonaria under unfavorable conditions were present in previously overlooked fractions of the microbiota. So far, unrecognized groups like Chthoniobacterales (Verrucomicrobia) emerged as functional protectors in the lichen microbiome. By combining multi-omics and imaging techniques, we highlight previously overlooked participants in the complex microenvironment of the lichens.

  11. Omics-Based Strategies in Precision Medicine: Toward a Paradigm Shift in Inborn Errors of Metabolism Investigations

    Directory of Open Access Journals (Sweden)

    Abdellah Tebani

    2016-09-01

    Full Text Available The rise of technologies that simultaneously measure thousands of data points represents the heart of systems biology. These technologies have had a huge impact on the discovery of next-generation diagnostics, biomarkers, and drugs in the precision medicine era. Systems biology aims to achieve systemic exploration of complex interactions in biological systems. Driven by high-throughput omics technologies and the computational surge, it enables multi-scale and insightful overviews of cells, organisms, and populations. Precision medicine capitalizes on these conceptual and technological advancements and stands on two main pillars: data generation and data modeling. High-throughput omics technologies allow the retrieval of comprehensive and holistic biological information, whereas computational capabilities enable high-dimensional data modeling and, therefore, accessible and user-friendly visualization. Furthermore, bioinformatics has enabled comprehensive multi-omics and clinical data integration for insightful interpretation. Despite their promise, the translation of these technologies into clinically actionable tools has been slow. In this review, we present state-of-the-art multi-omics data analysis strategies in a clinical context. The challenges of omics-based biomarker translation are discussed. Perspectives regarding the use of multi-omics approaches for inborn errors of metabolism (IEM are presented by introducing a new paradigm shift in addressing IEM investigations in the post-genomic era.

  12. Omics-Based Strategies in Precision Medicine: Toward a Paradigm Shift in Inborn Errors of Metabolism Investigations.

    Science.gov (United States)

    Tebani, Abdellah; Afonso, Carlos; Marret, Stéphane; Bekri, Soumeya

    2016-09-14

    The rise of technologies that simultaneously measure thousands of data points represents the heart of systems biology. These technologies have had a huge impact on the discovery of next-generation diagnostics, biomarkers, and drugs in the precision medicine era. Systems biology aims to achieve systemic exploration of complex interactions in biological systems. Driven by high-throughput omics technologies and the computational surge, it enables multi-scale and insightful overviews of cells, organisms, and populations. Precision medicine capitalizes on these conceptual and technological advancements and stands on two main pillars: data generation and data modeling. High-throughput omics technologies allow the retrieval of comprehensive and holistic biological information, whereas computational capabilities enable high-dimensional data modeling and, therefore, accessible and user-friendly visualization. Furthermore, bioinformatics has enabled comprehensive multi-omics and clinical data integration for insightful interpretation. Despite their promise, the translation of these technologies into clinically actionable tools has been slow. In this review, we present state-of-the-art multi-omics data analysis strategies in a clinical context. The challenges of omics-based biomarker translation are discussed. Perspectives regarding the use of multi-omics approaches for inborn errors of metabolism (IEM) are presented by introducing a new paradigm shift in addressing IEM investigations in the post-genomic era.

  13. Research on inbreeding in the 'omic' era

    DEFF Research Database (Denmark)

    Kristensen, Torsten N; Pedersen, Kamilla S; Vermeulen, Cornelis J

    2010-01-01

    Developments in molecular and systems biology have enabled novel approaches to be used in the study of inbreeding. Mechanistic and functional studies using ‘omic' technologies can increase the understanding of the consequences of inbreeding, from the level of DNA to that of population growth...

  14. Detector system of the first focal plane of the spectrometer SMART at RIKEN

    International Nuclear Information System (INIS)

    Okamura, H.; Izshida, S.; Sakamoto, N.; Otsu, H.; Uesaka, T.; Wakasa, T.; Satou, Y.; Sakai, H.; Ichihara, T.

    1998-01-01

    A detector system of the first focal plane of SMART, the 135 MeV/u high-resolution spectrometer at RIKEN accelerator research facility, is described. It consists of a pair of multi-wire drift chambers and a trigger scintillator hodoscope contained in a He-filled detector box. A major subject using this system is the measurement of the (d, 2 He) reaction making the most of its large angular and momentum acceptances. Without seriously sacrificing the detection efficiency, reasonably good energy and angular resolutions for 2 He, 460 keV and 9 mrad (FWHM), respectively, have been achieved after optimizing the optics property of the spectrometer. (orig.)

  15. Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants

    Czech Academy of Sciences Publication Activity Database

    Großkinsky, D.K.; Syaifullah, S. J.; Roitsch, Thomas

    2017-01-01

    Roč. 99, č. 99 (2017), s. 1-20 ISSN 0022-0957 R&D Projects: GA MŠk(CZ) LO1415 Institutional support: RVO:67179843 Keywords : integrated approaches * multi-omics * phenomics * plant development * plant–environment interactions * plant phenotyping * plant physiology * plant senescence * senescence programme * systems biology Subject RIV: EH - Ecology, Behaviour OBOR OECD: Environmental sciences (social aspects to be 5.7) Impact factor: 5.830, year: 2016

  16. Omics on bioleaching: current and future impacts.

    Science.gov (United States)

    Martinez, Patricio; Vera, Mario; Bobadilla-Fazzini, Roberto A

    2015-10-01

    Bioleaching corresponds to the microbial-catalyzed process of conversion of insoluble metals into soluble forms. As an applied biotechnology globally used, it represents an extremely interesting field of research where omics techniques can be applied in terms of knowledge development, but moreover in terms of process design, control, and optimization. In this mini-review, the current state of genomics, proteomics, and metabolomics of bioleaching and the major impacts of these analytical methods at industrial scale are highlighted. In summary, genomics has been essential in the determination of the biodiversity of leaching processes and for development of conceptual and functional metabolic models. Proteomic impacts are mostly related to microbe-mineral interaction analysis, including copper resistance and biofilm formation. Early steps of metabolomics in the field of bioleaching have shown a significant potential for the use of metabolites as industrial biomarkers. Development directions are given in order to enhance the future impacts of the omics in biohydrometallurgy.

  17. Molecular signatures from omics data: from chaos to consensus.

    Science.gov (United States)

    Sung, Jaeyun; Wang, Yuliang; Chandrasekaran, Sriram; Witten, Daniela M; Price, Nathan D

    2012-08-01

    In the past 15 years, new "omics" technologies have made it possible to obtain high-resolution molecular snapshots of organisms, tissues, and even individual cells at various disease states and experimental conditions. It is hoped that these developments will usher in a new era of personalized medicine in which an individual's molecular measurements are used to diagnose disease, guide therapy, and perform other tasks more accurately and effectively than is possible using standard approaches. There now exists a vast literature of reported "molecular signatures". However, despite some notable exceptions, many of these signatures have suffered from limited reproducibility in independent datasets, insufficient sensitivity or specificity to meet clinical needs, or other challenges. In this paper, we discuss the process of molecular signature discovery on the basis of omics data. In particular, we highlight potential pitfalls in the discovery process, as well as strategies that can be used to increase the odds of successful discovery. Despite the difficulties that have plagued the field of molecular signature discovery, we remain optimistic about the potential to harness the vast amounts of available omics data in order to substantially impact clinical practice. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Would Virchow be a systems biologist? A discourse on the philosophy of science with implications for pathological research.

    Science.gov (United States)

    Stenzinger, Albrecht; Klauschen, Frederick; Wittschieber, Daniel; Weichert, Wilko; Denkert, Carsten; Dietel, Manfred; Roller, Claudio

    2010-06-01

    Research in pathology spans from merely descriptive work to functional studies, "-omics" approaches and, more recently, systems biology. The work presented here aims at placing pathological research into an epistemological context. Aided by Rudolf Virchow, we give an overview on the philosophy of science including the Wiener Kreis, Popper, Kuhn, Fleck and Rheinberger and demonstrate their implications for routine diagnostics and science in pathology. A focus is on the fields of "-omics" and systems pathology.

  19. Shielding design of RIKEN RI Beam Factory

    Energy Technology Data Exchange (ETDEWEB)

    Uwamino, Yoshitomo; Fukunishi, Nobuhisa [Institute of Physical and Chemical Research, Wako, Saitama (Japan); Oishi, Koji [Shimizu Corp., Tokyo (Japan)

    2000-03-01

    Construction of the RIKEN RI Beam Factory is started, and the phase 1 will be finished by the end of March 2003. Two ring cyclotrons including one superconducting machine and two Big RIPSs will be constructed in the phase 1. Heavy ions of proton to uranium will be accelerated up to 400 MeV/u (A<40) and 150 MeV/u for uranium at an intensity of 10{sup 13} pps. Neutron production by the 400 MeV/u {sup 20}Ne beam was measured at HIMAC of NIRS and it was used for the source term of the shielding calculations. The deep penetration of high-energy neutrons was calculated by using the ANISN code with the DLC-119/HILO86R group constants and also by using the HETC code. The ANISN results were modified by using the HETC results and the shielding experiment at ISIS, and they were fitted by a simple formula for practical use. High-energy neutron penetrations of slantwise injection and the reflection probabilities of iron slab were calculated with the HETC code, and these results were used for the estimation of the thickness for the iron local shielding of Big RIPSs. Induced radioactivity in the air, accelerator components and the building, and the skyshine effect were also estimated. (author)

  20. Horizon Scanning: How Will Metabolomics Applications Transform Food Science, Bioengineering, and Medical Innovation in the Current Era of Foodomics?

    Science.gov (United States)

    Bayram, Mustafa; Gökırmaklı, Çağlar

    2018-03-01

    Food and engineering sciences have tended to neglect the importance of human nutrition sciences and clinical study of new molecules discovered by food engineering community, and vice versa. Yet, the value of systems thinking and use of omics technologies in food engineering are rapidly emerging. Foodomics is a new concept and practice to bring about "precision nutrition" and integrative bioengineering studies of food composition, quality, and safety, and applications to improve health of humans, animals, and other living organisms on the planet. Foodomics signals a three-way convergence among (1) food engineering; (2) omics systems science technologies such as proteomics, metabolomics, glycomics; and (3) medical/life sciences. This horizon scanning expert review aims to challenge the current practices in food sciences and bioengineering so as to adopt foodomics and systems thinking in foodstuff analysis, with a focus on possible applications of metabolomics. Among the omics biotechnologies, metabolomics is one of the prominent analytical platforms of interest to both food engineers and medical researchers engaged in nutritional sciences, precision medicine, and systems medicine diagnostics. Medical and omics system scientists, and bioengineering scholars can mutually learn from their respective professional expertise. Moving forward, establishment of "Foodomics Think Tanks" is one conceivable strategy to integrate medical and food sciences innovation at a systems scale. With its rich history in food sciences and tradition of interdisciplinary scholarship, the Silk Road countries offer notable potential for synthesis of diverse knowledge strands necessary to realize the prospects of foodomics from Asia and Middle East to Europe.

  1. Beam orbit in the central region of the RIKEN AVF cyclotron

    International Nuclear Information System (INIS)

    Toprek, D.; Subotic, K.; Goto, A.; Yano, Y.

    1998-01-01

    This paper describes the modification design of the central region for h=2 mode of acceleration in the RIKEN AVF cyclotron. The central region is equipped with an axial injection system. The spiral type inflector is used for axial injection. The electric field distribution in the inflector and in four acceleration gaps has been numerically calculated from an electric potential map produced by the program RELAX3D. The magnetic field is measured. The geometry of the central region has been tested with the computations of orbits carried out by means of the computer code CYCLONE. The optical properties of the spiral inflector and the central region are studied by using the program CASINO and CYCLONE, respectively. We have also made an effort to minimize the inflector fringe field using the RELAX3D program. (author)

  2. Predictive analytics of environmental adaptability in multi-omic network models.

    Science.gov (United States)

    Angione, Claudio; Lió, Pietro

    2015-10-20

    Bacterial phenotypic traits and lifestyles in response to diverse environmental conditions depend on changes in the internal molecular environment. However, predicting bacterial adaptability is still difficult outside of laboratory controlled conditions. Many molecular levels can contribute to the adaptation to a changing environment: pathway structure, codon usage, metabolism. To measure adaptability to changing environmental conditions and over time, we develop a multi-omic model of Escherichia coli that accounts for metabolism, gene expression and codon usage at both transcription and translation levels. After the integration of multiple omics into the model, we propose a multiobjective optimization algorithm to find the allowable and optimal metabolic phenotypes through concurrent maximization or minimization of multiple metabolic markers. In the condition space, we propose Pareto hypervolume and spectral analysis as estimators of short term multi-omic (transcriptomic and metabolic) evolution, thus enabling comparative analysis of metabolic conditions. We therefore compare, evaluate and cluster different experimental conditions, models and bacterial strains according to their metabolic response in a multidimensional objective space, rather than in the original space of microarray data. We finally validate our methods on a phenomics dataset of growth conditions. Our framework, named METRADE, is freely available as a MATLAB toolbox.

  3. Construction of a beam rebuncher for RIKEN RI-beam factory

    International Nuclear Information System (INIS)

    Aoki, T.; Stingelin, L.; Kamigaito, O.; Sakamoto, N.; Fukunishi, N.; Yokouchi, S.; Maie, T.; Kase, M.; Goto, A.; Yano, Y.

    2008-01-01

    A beam rebuncher for the RIKEN radioactive-isotope beam factory project has been constructed and is placed in a long beam line between the first two ring cyclotrons in the accelerator cascade. The rebuncher resonator, having four rf gaps in it, operates at a fixed frequency of 109.5 MHz for the longitudinal focusing of heavy ion beams at 11.0MeV/u. To reduce the sparking problem in the rf gaps, a new type of H-mode resonator has been adopted, where the distribution of the gap voltage is well equalized. In fact, the ratio of the gap voltages is about 1.26, whereas those of the interdigital-H (IH)- and crossed-bar-H (CH)-mode structures are larger than 2.0. The total gap voltage, which is defined as the sum of the four gap voltages, has reached 495 kV at a power consumption of 4.7 kW

  4. OMICS and 21st century brain surgery from education to practice: James Rutka of the University of Toronto interviewed by Joseph B. Martin (Boston) and Türker Kılıç (İstanbul).

    Science.gov (United States)

    Rutka, James; Martin, Joseph; Kılıç, Türker

    2014-12-01

    The Science-in-Backstage interviews aim to share experiences by global medical and life sciences thought leaders on emergent technologies and novel scientific, medical, and educational practices, situating them in both a historical and contemporary science context so as to "look into the biotechnology and innovation futures" reflexively and intelligently. OMICS systems diagnostics and personalized medicine are greatly impacting brain surgery, not to forget the training of the next generation of neurosurgeons. What do the futures hold for the practice of, and education in 21(st) century brain surgery in the age of OMICS systems science, personalized medicine, and the use of simulation in surgeon training? James Rutka is a clinician scientist and a world leader in diagnosis and treatment of brain tumors. He is Professor and Chair of the Department of Surgery at the Faculty of Medicine, University of Toronto, a President Emeritus of the American Association of Neurological Surgeons, and Editor-in-Chief of the Journal of Neurosurgery. Professor Rutka was interviewed for the global medical, biotechnology, and life sciences readership of the OMICS: A Journal of Integrative Biology to speak on these pressing questions in his personal capacity as an independent senior scholar. The issues debated in the present interview are of broad relevance for 21(st) century surgery and postgenomics medicine. The interviewers were Professor Joseph B. Martin, Harvard Medical School Dean Emeritus in Boston and Joint Dean of Medicine at Bahçeşehir University in İstanbul, and the author of "Alfalfa to Ivy: Memoir of a Harvard Medical School Dean," and Professor Türker Kılıç, Dean of Medicine at Bahçeşehir University in İstanbul, and an elected member of the Turkish Academy of Sciences.

  5. CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002

    OpenAIRE

    Yang, Yaohua; Feng, Jie; Li, Tao; Ge, Feng; Zhao, Jindong

    2015-01-01

    Cyanobacteria are an important group of organisms that carry out oxygenic photosynthesis and play vital roles in both the carbon and nitrogen cycles of the Earth. The annotated genome of Synechococcus sp. PCC 7002, as an ideal model cyanobacterium, is available. A series of transcriptomic and proteomic studies of Synechococcus sp. PCC 7002 cells grown under different conditions have been reported. However, no database of such integrated omics studies has been constructed. Here we present Cyan...

  6. Omics-bioinformatics in the context of clinical data

    NARCIS (Netherlands)

    Mayer, Gert; Heinze, Georg; Mischak, Harald; Hellemons, Merel E; Heerspink, Hiddo J Lambers; Bakker, Stephan J L; de Zeeuw, Dick; Haiduk, Martin; Rossing, Peter; Oberbauer, Rainer

    2011-01-01

    The Omics revolution has provided the researcher with tools and methodologies for qualitative and quantitative assessment of a wide spectrum of molecular players spanning from the genome to the meta-bolome level. As a consequence, explorative analysis (in contrast to purely hypothesis driven

  7. News in livestock research — use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals

    Directory of Open Access Journals (Sweden)

    Simon Deusch

    2015-01-01

    This review will provide a general overview about the recent Omics-based research of the microbiota in livestock including its major findings. Differences concerning the results of pre-Omics-approaches in livestock as well as the perspectives of this relatively new Omics-platform will be highlighted.

  8. DTW4Omics: comparing patterns in biological time series.

    Directory of Open Access Journals (Sweden)

    Rachel Cavill

    Full Text Available When studying time courses of biological measurements and comparing these to other measurements eg. gene expression and phenotypic endpoints, the analysis is complicated by the fact that although the associated elements may show the same patterns of behaviour, the changes do not occur simultaneously. In these cases standard correlation-based measures of similarity will fail to find significant associations. Dynamic time warping (DTW is a technique which can be used in these situations to find the optimal match between two time courses, which may then be assessed for its significance. We implement DTW4Omics, a tool for performing DTW in R. This tool extends existing R scripts for DTW making them applicable for "omics" datasets where thousands entities may need to be compared with a range of markers and endpoints. It includes facilities to estimate the significance of the matches between the supplied data, and provides a set of plots to enable the user to easily visualise the output. We illustrate the utility of this approach using a dataset linking the exposure of the colon carcinoma Caco-2 cell line to oxidative stress by hydrogen peroxide (H2O2 and menadione across 9 timepoints and show that on average 85% of the genes found are not obtained from a standard correlation analysis between the genes and the measured phenotypic endpoints. We then show that when we analyse the genes identified by DTW4Omics as significantly associated with a marker for oxidative DNA damage (8-oxodG, through over-representation, an Oxidative Stress pathway is identified as the most over-represented pathway demonstrating that the genes found by DTW4Omics are biologically relevant. In contrast, when the positively correlated genes were similarly analysed, no pathways were found. The tool is implemented as an R Package and is available, along with a user guide from http://web.tgx.unimaas.nl/svn/public/dtw/.

  9. Omics-based nanomedicine: the future of personalized oncology.

    Science.gov (United States)

    Rosenblum, Daniel; Peer, Dan

    2014-09-28

    The traditional "one treatment fits all" paradigm disregards the heterogeneity between cancer patients, and within a particular tumor, thus limit the success of common treatments. Moreover, current treatment lacks specificity and therefore most of the anticancer drugs induce severe adverse effects. Personalized medicine aims to individualize therapeutic interventions, based on the growing knowledge of the human multiple '-oms' (e.g. genome, epigenome, transcriptome, proteome and metabolome), which has led to the discovery of various biomarkers that can be used to detect early stage cancers and predict tumor progression, drug response, and clinical outcome. Nanomedicine, the application of nanotechnology to healthcare, holds great promise for revolutionizing disease management such as drug delivery, molecular imaging, reduced adverse effects and the ability to contain both therapeutic and diagnostic modalities simultaneously termed theranostics. Personalizednanomedicine has the power of combining nanomedicine with clinical and molecular biomarkers ("OMICS" data) achieving improve prognosis and disease management as well as individualized drug selection and dosage profiling to ensure maximal efficacy and safety. Tumor's heterogeneity sets a countless challenge for future personalized therapy in cancer, however the use of multi-parameter 'omic's data for specific molecular biomarkers recognition together with versatile drug delivery nanocarriers, which could target concomitantly and specifically tumor cells subpopulations, might heralds a brighter future for personalized cancer management. In this review, we present the current leading technologies available for personalized oncology. We discusses the immense potential of combining the best of these two worlds, nanomedicine and high throughput OMICS technologies to pave the way towards cancer personalized medicine. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  10. Perspective for Aquaponic Systems: "Omic" Technologies for Microbial Community Analysis.

    Science.gov (United States)

    Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Torres-Pacheco, Irineo; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V; Garcia-Trejo, Juan F; Guevara-Gonzalez, Ramon G

    2015-01-01

    Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the "Omic" technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. "Omic" technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current "Omic" tools to characterize the microbial community in aquaponic systems.

  11. Biomolecular Analysis Capability for Cellular and Omics Research on the International Space Station

    Science.gov (United States)

    Guinart-Ramirez, Y.; Cooley, V. M.; Love, J. E.

    2016-01-01

    International Space Station (ISS) assembly complete ushered a new era focused on utilization of this state-of-the-art orbiting laboratory to advance science and technology research in a wide array of disciplines, with benefits to Earth and space exploration. ISS enabling capability for research in cellular and molecular biology includes equipment for in situ, on-orbit analysis of biomolecules. Applications of this growing capability range from biomedicine and biotechnology to the emerging field of Omics. For example, Biomolecule Sequencer is a space-based miniature DNA sequencer that provides nucleotide sequence data for entire samples, which may be used for purposes such as microorganism identification and astrobiology. It complements the use of WetLab-2 SmartCycler"TradeMark", which extracts RNA and provides real-time quantitative gene expression data analysis from biospecimens sampled or cultured onboard the ISS, for downlink to ground investigators, with applications ranging from clinical tissue evaluation to multigenerational assessment of organismal alterations. And the Genes in Space-1 investigation, aimed at examining epigenetic changes, employs polymerase chain reaction to detect immune system alterations. In addition, an increasing assortment of tools to visualize the subcellular distribution of tagged macromolecules is becoming available onboard the ISS. For instance, the NASA LMM (Light Microscopy Module) is a flexible light microscopy imaging facility that enables imaging of physical and biological microscopic phenomena in microgravity. Another light microscopy system modified for use in space to image life sciences payloads is initially used by the Heart Cells investigation ("Effects of Microgravity on Stem Cell-Derived Cardiomyocytes for Human Cardiovascular Disease Modeling and Drug Discovery"). Also, the JAXA Microscope system can perform remotely controllable light, phase-contrast, and fluorescent observations. And upcoming confocal microscopy

  12. Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes.

    Science.gov (United States)

    Hultman, Jenni; Waldrop, Mark P; Mackelprang, Rachel; David, Maude M; McFarland, Jack; Blazewicz, Steven J; Harden, Jennifer; Turetsky, Merritt R; McGuire, A David; Shah, Manesh B; VerBerkmoes, Nathan C; Lee, Lang Ho; Mavrommatis, Kostas; Jansson, Janet K

    2015-05-14

    Over 20% of Earth's terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils and a rapid shift in functional gene composition during short-term thaw experiments. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales. Here we use the combination of several molecular 'omics' approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.

  13. Air Force Research Laboratory Integrated Omics Research

    Science.gov (United States)

    2015-10-01

    fuel exposures and cognitive fatigue. 15. SUBJECT TERMS biomonitoring, omics, metabonomics, proteomics, genomics, epigenetics, biomarker, toxin...biomarker discovery in a number of toxicology and human performance projects, including jet fuel exposures and cognitive fatigue. INTRODUCTION One of...chemical exposure for U.S. and NATO military personnel46; inhalation and dermal have been shown to represent the primary routes of exposure47 This

  14. Influenza-Omics and the Host Response: Recent Advances and Future Prospects

    Science.gov (United States)

    Powell, Joshua D.; Waters, Katrina M.

    2017-01-01

    Influenza A viruses (IAV) continually evolve and have the capacity to cause global pandemics. Because IAV represents an ongoing threat, identifying novel therapies and host innate immune factors that contribute to IAV pathogenesis is of considerable interest. This review summarizes the relevant literature as it relates to global host responses to influenza infection at both the proteome and transcriptome level. The various-omics infection systems that include but are not limited to ferrets, mice, pigs, and even the controlled infection of humans are reviewed. Discussion focuses on recent advances, remaining challenges, and knowledge gaps as it relates to influenza-omics infection outcomes. PMID:28604586

  15. Evaluation of O2PLS in Omics data integration

    NARCIS (Netherlands)

    el Bouhaddani, S.; Houwing-Duistermaat, Jeanine; Salo, Perttu; Perola, Markus; Jongbloed, G.; Uh, Hae-Won

    2016-01-01

    Background
    Rapid computational and technological developments made large amounts of omics data available in different biological levels. It is becoming clear that simultaneous data analysis methods are needed for better interpretation and understanding of the underlying systems biology.

  16. Beam Orbit Simulation In The Central Region Of The Riken Avf Cyclotron

    International Nuclear Information System (INIS)

    Toprek, D; Subotic, K.; Goto, A.; Yano, Y.

    1998-01-01

    This paper describes the modification design of the central region for A = 2 mode of acceleration in the Riken Avf cyclotron. The central region is equipped with an axial injection system. The spiral type inflector is used for axial injection. The electric field distribution in the inflector and in four acceleration gaps has been numerically calculated from an electric potential map produced by the program RELAX3D. The magnetic field is measured. The geometry of the central region has been tested with the computations of orbits carried out by means of the computer code CYCLONE. The optical properties of the spiral inflector and the central region are studied by using the program CASINO and CYCLONE, respectively. We have also made an effort to minimize the inflector fringe field using the RELAX3D program. (authors)

  17. Beam orbit simulation in the central region of the RIKEN AVF cyclotron

    International Nuclear Information System (INIS)

    Toprek, Dragan; Goto, Akira; Yano, Yasushige

    1997-01-01

    This paper describes the modification design of the central region for h = 2 mode of acceleration in the RIKEN AVF cyclotron. The central region is equipped with an axial injection system. The spiral type inflector is used for axial injection. The electric field distribution in the inflector and in four acceleration gaps has been numerically calculated from an electric potential map produced by the program RELAX3D. The magnetic field is measured. The geometry of the central region has been tested with the computations of orbits carried out by means of the computer code CYCLONE. The optical properties of the spiral inflector and the central region are studied by using the program CASINO and CYCLONE, respectively. We have also made an effort to minimize the inflector fringe field using the RELAX3D program. (author)

  18. Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology.

    Science.gov (United States)

    Fondi, Marco; Liò, Pietro

    2015-02-01

    Integrated -omics approaches are quickly spreading across microbiology research labs, leading to (i) the possibility of detecting previously hidden features of microbial cells like multi-scale spatial organization and (ii) tracing molecular components across multiple cellular functional states. This promises to reduce the knowledge gap between genotype and phenotype and poses new challenges for computational microbiologists. We underline how the capability to unravel the complexity of microbial life will strongly depend on the integration of the huge and diverse amount of information that can be derived today from -omics experiments. In this work, we present opportunities and challenges of multi -omics data integration in current systems biology pipelines. We here discuss which layers of biological information are important for biotechnological and clinical purposes, with a special focus on bacterial metabolism and modelling procedures. A general review of the most recent computational tools for performing large-scale datasets integration is also presented, together with a possible framework to guide the design of systems biology experiments by microbiologists. Copyright © 2015. Published by Elsevier GmbH.

  19. Proceedings of RIKEN BNL Research Center Workshop, RHIC Spin Physics V, Volume 32, February 21, 2001

    International Nuclear Information System (INIS)

    BUNCE, G.; SAITO, N.; VIGDOR, S.; ROSER, T.; SPINKA, H.; ENYO, H.; BLAND, L.C.; GURYN, W.

    2001-01-01

    The RIKEN BNL Research Center (RBRC) was established in April 1997 at Brookhaven National Laboratory. It is funded by the ''Rikagaku Kenkysho'' (RIKEN, The Institute of Physical and Chemical Research) of Japan. The Center is dedicated to the study of strong interactions, including spin physics, lattice QCD and RHIC physics through the nurturing of a new generation of young physicists. During the fast year, the Center had only a Theory Group. In the second year, an Experimental Group was also established at the Center. At present, there are seven Fellows and nine post dots in these two groups. During the third year, we started a new Tenure Track Strong Interaction Theory RHIC Physics Fellow Program, with six positions in the academic year 1999-2000; this program will increase to include eleven theorists in the next academic year, and, in the year after, also be extended to experimental physics. In addition, the Center has an active workshop program on strong interaction physics, about ten workshops a year, with each workshop focused on a specific physics problem. Each workshop speaker is encouraged to select few of the most important transparencies from his or her presentation, accompanied by a page of explanation. This material is collected at the end of the workshop by the organizer to form proceedings, which can therefore be available within a short time. The construction of a 0.6 teraflop parallel processor, which was begun at the Center on February 19, 1998, was completed on August 28, 1998

  20. Status and results from the decay spectroscopy project EURICA (Euroball-RIKEN cluster array)

    Energy Technology Data Exchange (ETDEWEB)

    Söderström, P.-A., E-mail: pasoder@ribf.riken.jp; Doornenbal, P.; Nishimura, S.; Baba, H.; Isobe, T.; Kiss, G. [RIKEN Nishina Center, 2-1 Hirosawa, Wako-shi, Saitama 351-0198 (Japan); Lorusso, G. [RIKEN Nishina Center, 2-1 Hirosawa, Wako-shi, Saitama 351-0198 (Japan); National Physical Laboratory, Teddington, Middlesex, TW11 0LW (United Kingdom); Wu, J. [RIKEN Nishina Center, 2-1 Hirosawa, Wako-shi, Saitama 351-0198 (Japan); School of Physics, Peking University, Beijing 100871 (China); Xu, Z. Y. [Department of Physics, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); KU Leuven, Instituut voor Kern-en Stralingsfysica, 3001 Leuven (Belgium); Benzoni, G. [Istituto Nazionale di Fisica Nucleare, Sezione di Milano, Via Celoria 16, 20133 Milano (Italy); Browne, F. [RIKEN Nishina Center, 2-1 Hirosawa, Wako-shi, Saitama 351-0198 (Japan); School of Computing, Engineering and Mathematics, University of Brighton, Brighton BN2 4JG (United Kingdom); Gey, G. [RIKEN Nishina Center, 2-1 Hirosawa, Wako-shi, Saitama 351-0198 (Japan); LPSC, Université Grenoble-Alpes, CNRS/IN2P3, F-38026 Grenoble Cedex (France); ILL, 38042 Grenoble Cedex (France); Research Center for Nuclear Physics (RCNP), Osaka University, Ibaraki, Osaka 567-0047 (Japan); Jungclaus, A. [Instituto de Estructura de la Materia, CSIC, E-28006 Madrid (Spain); Kojouharov, I.; Kurz, N.; Schaffner, H. [GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt (Germany); Lubos, D. [RIKEN Nishina Center, 2-1 Hirosawa, Wako-shi, Saitama 351-0198 (Japan); Physik Department E12, Technische Universität München, D-85748 Garching (Germany); Moschner, K. [RIKEN Nishina Center, 2-1 Hirosawa, Wako-shi, Saitama 351-0198 (Japan); IKP, University of Cologne, D-50937 Cologne (Germany); and others

    2016-07-07

    β- and isomer-decay spectroscopy are sensitive probes of nuclear structure, and are often the only techniques capable of providing data for exotic nuclei that are produced with very low rates. Decay properties of exotic nuclei are also essential to model astrophysical events responsible for the evolution of the universe such as the rp- and r-processes. The EURICA project (EUROBALL RIKEN Cluster Array) has been launched in 2012 with the goal of performing spectroscopy of very exotic nuclei. Since 2012, five experimental campaigns have been successfully completed using fragmentation of {sup 124}Xe beam and in-flight-fission of {sup 238}U beam. In these proceedings we will introduce the experimental setup and highlight some key recent results around {sup 78}Ni, {sup 132}Sn, and {sup 110}Zn published during 2014 and 2015.

  1. Multi-omic data integration enables discovery of hidden biological regularities

    DEFF Research Database (Denmark)

    Ebrahim, Ali; Brunk, Elizabeth; Tan, Justin

    2016-01-01

    Rapid growth in size and complexity of biological data sets has led to the 'Big Data to Knowledge' challenge. We develop advanced data integration methods for multi- level analysis of genomic, transcriptomic, ribosomal profiling, proteomic and fluxomic data. First, we show that pairwise integration...... of primary omics data reveals regularities that tie cellular processes together in Escherichia coli: the number of protein molecules made per mRNA transcript and the number of ribosomes required per translated protein molecule. Second, we show that genome- scale models, based on genomic and bibliomic data......, enable quantitative synchronization of disparate data types. Integrating omics data with models enabled the discovery of two novel regularities: condition invariant in vivo turnover rates of enzymes and the correlation of protein structural motifs and translational pausing. These regularities can...

  2. Single-cell technologies in environmental omics

    KAUST Repository

    Kodzius, Rimantas

    2015-10-22

    Environmental studies are primarily done by culturing isolated microorganisms or by amplifying and sequencing conserved genes. Difficulties understanding the complexity of large numbers of various microorganisms in an environment led to the development of techniques to enrich specific microorganisms for upstream analysis, ultimately leading to single-cell isolation and analyses. We discuss the significance of single-cell technologies in omics studies with focus on metagenomics and metatranscriptomics. We propose that by reducing sample heterogeneity using single-cell genomics, metaomic studies can be simplified.

  3. Single-cell technologies in environmental omics

    KAUST Repository

    Kodzius, Rimantas; Gojobori, Takashi

    2015-01-01

    Environmental studies are primarily done by culturing isolated microorganisms or by amplifying and sequencing conserved genes. Difficulties understanding the complexity of large numbers of various microorganisms in an environment led to the development of techniques to enrich specific microorganisms for upstream analysis, ultimately leading to single-cell isolation and analyses. We discuss the significance of single-cell technologies in omics studies with focus on metagenomics and metatranscriptomics. We propose that by reducing sample heterogeneity using single-cell genomics, metaomic studies can be simplified.

  4. The Twins Study: NASA's First Foray into 21st Century Omics Research

    Science.gov (United States)

    Kundrot, C. E.; Shelhamer, M.; Scott, G. B. I.

    2015-01-01

    The full array of 21st century omics-based research methods should be intelligently employed to reduce the health and performance risks that astronauts will be exposed to during exploration missions beyond low Earth Orbit. In March of 2015, US Astronaut Scott Kelly will launch to the International Space Station for a one year mission while his twin brother, Mark Kelly, a retired US Astronaut, remains on the ground. This situation presents an extremely rare flight opportunity to perform an integrated omics-based demonstration pilot study involving identical twin astronauts. A group of 10 principal investigators has been competitively selected, funded, and teamed together to form the Twins Study. A very broad range of biological function are being examined including the genome, epigenome, transcriptome, proteome, metabolome, gut microbiome, immunological response to vaccinations, indicators of atherosclerosis, physiological fluid shifts, and cognition. The plans for the Twins Study and an overview of initial results will be described as well as the technological and ethical issues raised for such spaceflight studies. An anticipated outcome of the Twins Study is that it will place NASA on a trajectory of using omics-based information to develop precision countermeasures for individual astronauts.

  5. Deep-Sea Microbes: Linking Biogeochemical Rates to -Omics Approaches

    Science.gov (United States)

    Herndl, G. J.; Sintes, E.; Bayer, B.; Bergauer, K.; Amano, C.; Hansman, R.; Garcia, J.; Reinthaler, T.

    2016-02-01

    Over the past decade substantial progress has been made in determining deep ocean microbial activity and resolving some of the enigmas in understanding the deep ocean carbon flux. Also, metagenomics approaches have shed light onto the dark ocean's microbes but linking -omics approaches to biogeochemical rate measurements are generally rare in microbial oceanography and even more so for the deep ocean. In this presentation, we will show by combining metagenomics, -proteomics and biogeochemical rate measurements on the bulk and single-cell level that deep-sea microbes exhibit characteristics of generalists with a large genome repertoire, versatile in utilizing substrate as revealed by metaproteomics. This is in striking contrast with the apparently rather uniform dissolved organic matter pool in the deep ocean. Combining the different -omics approaches with metabolic rate measurements, we will highlight some major inconsistencies and enigmas in our understanding of the carbon cycling and microbial food web structure in the dark ocean.

  6. TOMATOMICS: A Web Database for Integrated Omics Information in Tomato

    KAUST Repository

    Kudo, Toru; Kobayashi, Masaaki; Terashima, Shin; Katayama, Minami; Ozaki, Soichi; Kanno, Maasa; Saito, Misa; Yokoyama, Koji; Ohyanagi, Hajime; Aoki, Koh; Kubo, Yasutaka; Yano, Kentaro

    2016-01-01

    Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.

  7. TOMATOMICS: A Web Database for Integrated Omics Information in Tomato

    KAUST Repository

    Kudo, Toru

    2016-11-29

    Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.

  8. HEROD: a human ethnic and regional specific omics database.

    Science.gov (United States)

    Zeng, Xian; Tao, Lin; Zhang, Peng; Qin, Chu; Chen, Shangying; He, Weidong; Tan, Ying; Xia Liu, Hong; Yang, Sheng Yong; Chen, Zhe; Jiang, Yu Yang; Chen, Yu Zong

    2017-10-15

    Genetic and gene expression variations within and between populations and across geographical regions have substantial effects on the biological phenotypes, diseases, and therapeutic response. The development of precision medicines can be facilitated by the OMICS studies of the patients of specific ethnicity and geographic region. However, there is an inadequate facility for broadly and conveniently accessing the ethnic and regional specific OMICS data. Here, we introduced a new free database, HEROD, a human ethnic and regional specific OMICS database. Its first version contains the gene expression data of 53 070 patients of 169 diseases in seven ethnic populations from 193 cities/regions in 49 nations curated from the Gene Expression Omnibus (GEO), the ArrayExpress Archive of Functional Genomics Data (ArrayExpress), the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Geographic region information of curated patients was mainly manually extracted from referenced publications of each original study. These data can be accessed and downloaded via keyword search, World map search, and menu-bar search of disease name, the international classification of disease code, geographical region, location of sample collection, ethnic population, gender, age, sample source organ, patient type (patient or healthy), sample type (disease or normal tissue) and assay type on the web interface. The HEROD database is freely accessible at http://bidd2.nus.edu.sg/herod/index.php. The database and web interface are implemented in MySQL, PHP and HTML with all major browsers supported. phacyz@nus.edu.sg. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  9. Time-stamping system for nuclear physics experiments at RIKEN RIBF

    International Nuclear Information System (INIS)

    Baba, H.; Ichihara, T.; Ohnishi, T.; Takeuchi, S.; Yoshida, K.; Watanabe, Y.; Ota, S.; Shimoura, S.; Yoshinaga, K.

    2015-01-01

    A time-stamping system for nuclear physics experiments has been introduced at the RIKEN Radioactive Isotope Beam Factory. Individual trigger signals can be applied for separate data acquisition (DAQ) systems. After the measurements are complete, separately taken data are merged based on the time-stamp information. In a typical experiment, coincidence trigger signals are formed from multiple detectors to take desired events only. The time-stamping system allows the use of minimum bias triggers. Since coincidence conditions are given by software, a variety of physics events can be flexibly identified. The live time for a DAQ system is important when attempting to determine reaction cross-sections. However, the combined live time for separate DAQ systems is not clearly known because it depends not only on the DAQ dead time but also on the coincidence conditions. Using the proposed time-stamping system, all trigger timings can be acquired, so that the combined live time can be easily determined. The combined live time is also estimated using Monte Carlo simulations, and the results are compared with the directly measured values in order to assess the accuracy of the simulation

  10. Operating experiences on the co-generation system (CGS) as an uninterruptible power source (UPS) for the super-sized accelerator facility, RIBF of RIKEN

    International Nuclear Information System (INIS)

    Fujinawa, Tadashi; Yano, Yasushige

    2011-01-01

    The RI Beam Factory (RIBF) of RIKEN Nishina Center for Accelerator-Based Science, which succeeded in extracting first beam on December 28th 2006 as scheduled, is currently conducting nuclear physics experiments. The RIBF has six accelerators, one of which is the world's biggest and most powerful superconducting ring cyclotron (SRC). The accelerators require not only a huge amount of electricity but also a reliable power supply for the He-cryogenic system, vacuum system and superconducting magnet systems. For this purpose, the co-generation system (CGS) was introduced. A gas turbine generates 6.5 MW of power from liquid natural gas (LNG) and supplies it to the systems mentioned above as an uninterruptible power source (UPS). By utilizing gas heat exhaust from the gas turbine, the CGS will also supply cooled water to the cooling system of the RIBF accelerators as well as to the air-conditioning system for the bending. The CGS plant was completed on the 1st floor of the RIBF accelerator building and it began operating in April 2003. This paper covers the merits and demerits. (author)

  11. Enhancement of Ar sup 8 sup + ion beam intensity from RIKEN 18 GHz electron cyclotron resonance ion source by optimizing the magnetic field configuration

    CERN Document Server

    Higurashi, Y; Kidera, M; Kase, M; Yano, Y; Aihara, T

    2003-01-01

    We successfully produced a 1.55 emA Ar sup 8 sup + ion beam using the RIKEN 18 GHz electron cyclotron resonance ion source at a microwave power of 700 W. To produce such an intense beam, we optimized the minimum magnetic field of mirror magnetic field and plasma electrode position. (author)

  12. Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates

    Directory of Open Access Journals (Sweden)

    Silva Holtfreter

    2016-03-01

    Full Text Available Staphylococcus aureus is a dangerous pathogen both in hospitals and in the community. Due to the crisis of antibiotic resistance, there is an urgent need for new strategies to combat S. aureus infections, such as vaccination. Increasing our knowledge about the mechanisms of protection will be key for the successful prevention or treatment of S. aureus invasion. Omics technologies generate a comprehensive picture of the physiological and pathophysiological processes within cells, tissues, organs, organisms and even populations. This review provides an overview of the contribution of genomics, transcriptomics, proteomics, metabolomics and immunoproteomics to the current understanding of S. aureus‑host interaction, with a focus on the adaptive immune response to the microorganism. While antibody responses during colonization and infection have been analyzed in detail using immunoproteomics, the full potential of omics technologies has not been tapped yet in terms of T-cells. Omics technologies promise to speed up vaccine development by enabling reverse vaccinology approaches. In consequence, omics technologies are powerful tools for deepening our understanding of the “superbug” S. aureus and for improving its control.

  13. Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates

    Science.gov (United States)

    Holtfreter, Silva; Kolata, Julia; Stentzel, Sebastian; Bauerfeind, Stephanie; Schmidt, Frank; Sundaramoorthy, Nandakumar; Bröker, Barbara M.

    2016-01-01

    Staphylococcus aureus is a dangerous pathogen both in hospitals and in the community. Due to the crisis of antibiotic resistance, there is an urgent need for new strategies to combat S. aureus infections, such as vaccination. Increasing our knowledge about the mechanisms of protection will be key for the successful prevention or treatment of S. aureus invasion. Omics technologies generate a comprehensive picture of the physiological and pathophysiological processes within cells, tissues, organs, organisms and even populations. This review provides an overview of the contribution of genomics, transcriptomics, proteomics, metabolomics and immunoproteomics to the current understanding of S. aureus‑host interaction, with a focus on the adaptive immune response to the microorganism. While antibody responses during colonization and infection have been analyzed in detail using immunoproteomics, the full potential of omics technologies has not been tapped yet in terms of T-cells. Omics technologies promise to speed up vaccine development by enabling reverse vaccinology approaches. In consequence, omics technologies are powerful tools for deepening our understanding of the “superbug” S. aureus and for improving its control. PMID:28248221

  14. RIKEN 200 kV high current implanter for metal surface modification

    International Nuclear Information System (INIS)

    Iwaki, M.; Yoshida, K.; Sakudo, N.

    1985-01-01

    A high current, metal ion implanter was constructed in order to aid the formation of a new metastable surface alloy. This implanter, called a RIKEN 200 kV high current implanter, is a modified Lintott high current machine (Series III), which has the advantages of having its own microwave ion source and an extra target chamber. The microwave discharge ion source without a hot-filament has a comparatively long lifetime because the chloride ions and radicals in a plasma during discharge of metal chlorides might prevent metal to deposit on the inner walls of the discharge chamber by bombarding and chemically cleaning them. An extra target chamber for metal modification is able to control the surface composition by utilizing the sputtering effect of the ion beam during ion implantation. The use of this ion source and the extra target chamber is suggested to be suitable for the production of metallic ions and for the implantation into metals. The case study will be introduced for TI implantation into Fe. (orig.)

  15. Beam orbit simulation in the central region of the RIKEN AVF cyclotron

    International Nuclear Information System (INIS)

    Toprek, Dragan; Goto, Akira; Yano, Yasushige

    1999-01-01

    This paper describes the modification design of the central region for h=2 mode of acceleration in the RIKEN AVF cyclotron. we made a small modification to the electrode shape in the central region for optimization of the beam transmission. The central region is equipped with an axial injection system. The spiral type inflector is used for axial injection. The electric field distribution in the inflector and in four acceleration gaps has been numerically calculated from an electric potential map produced by the program RELAX3D. The magnetic field is measured. The geometry of the central region has been tested with the computations of orbits carried out by means of the computer code CYCLONE. The optical properties of the spiral inflector and the central region are studied by using the program CASINO and CYCLONE, respectively. We have also made an effort to minimize the inflector fringe field effects using the RELAX3D program

  16. Beam orbit simulation in the central region of the RIKEN AVF cyclotron

    CERN Document Server

    Toprek, D; Yano, Y

    1999-01-01

    This paper describes the modification design of the central region for h=2 mode of acceleration in the RIKEN AVF cyclotron. we made a small modification to the electrode shape in the central region for optimization of the beam transmission. The central region is equipped with an axial injection system. The spiral type inflector is used for axial injection. The electric field distribution in the inflector and in four acceleration gaps has been numerically calculated from an electric potential map produced by the program RELAX3D. The magnetic field is measured. The geometry of the central region has been tested with the computations of orbits carried out by means of the computer code CYCLONE. The optical properties of the spiral inflector and the central region are studied by using the program CASINO and CYCLONE, respectively. We have also made an effort to minimize the inflector fringe field effects using the RELAX3D program.

  17. Measurement of the tensor analyzing powers in the dd→3Hen and dd→3Hp reactions at RIKEN

    International Nuclear Information System (INIS)

    Ladygin, V.P.; Ladygina, N.B; Sakai, H.; Uesaka, T.

    2000-01-01

    A new experiment is proposed to measure the angular distribution of the tensor analyzing powers A yy , A xx , and A xz in the dd→ 3 Hen and dd→ 3 Hp reactions using polarized deuteron beam at RIKEN. These polarization observables are sensitive to the spin-momentum distribution of neutron (proton) in 3 He( 3 H) at short distances in the framework of one-nucleon exchange approximation. These measurements will provide new insight into the 3-nucleon system spin structure at distances unreachable at the moment using electromagnetic probes

  18. Bernard Lerer: Recipient of the 2014 Inaugural Werner Kalow Responsible Innovation Prize in Global Omics and Personalized Medicine (Pacific Rim Association for Clinical Pharmacogenetics)

    Science.gov (United States)

    Aynacıoğlu, Şükrü; Bragazzi, Nicola Luigi; Dandara, Collet; Dove, Edward S.; Ferguson, Lynnette R.; Geraci, Christy Jo; Hafen, Ernst; Kesim, Belgin Eroğlu; Kolker, Eugene; Lee, Edmund J.D.; LLerena, Adrian; Nacak, Muradiye; Shimoda, Kazutaka; Someya, Toshiyuki; Srivastava, Sanjeeva; Tomlinson, Brian; Vayena, Effy; Warnich, Louise; Yaşar, Ümit

    2014-01-01

    Abstract This article announces the recipient of the 2014 inaugural Werner Kalow Responsible Innovation Prize in Global Omics and Personalized Medicine by the Pacific Rim Association for Clinical Pharmacogenetics (PRACP): Bernard Lerer, professor of psychiatry and director of the Biological Psychiatry Laboratory, Hadassah-Hebrew University Medical Center, Jerusalem, Israel. The Werner Kalow Responsible Innovation Prize is given to an exceptional interdisciplinary scholar who has made highly innovative and enduring contributions to global omics science and personalized medicine, with both vertical and horizontal (transdisciplinary) impacts. The prize is established in memory of a beloved colleague, mentor, and friend, the late Professor Werner Kalow, who cultivated the idea and practice of pharmacogenetics in modern therapeutics commencing in the 1950s. PRACP, the prize's sponsor, is one of the longest standing learned societies in the Asia-Pacific region, and was founded by Kalow and colleagues more than two decades ago in the then-emerging field of pharmacogenetics. In announcing this inaugural prize and its winner, we seek to highlight the works of prize winner, Professor Lerer. Additionally, we contextualize the significance of the prize by recalling the life and works of Professor Kalow and providing a brief socio-technical history of the rise of pharmacogenetics and personalized medicine as a veritable form of 21st century scientific practice. The article also fills a void in previous social science analyses of pharmacogenetics, by bringing to the fore the works of Kalow from 1995 to 2008, when he presciently noted the rise of yet another field of postgenomics inquiry—pharmacoepigenetics—that railed against genetic determinism and underscored the temporal and spatial plasticity of genetic components of drug response, with invention of the repeated drug administration (RDA) method that estimates the dynamic heritabilities of drug response. The prize goes a

  19. Current dichotomy between traditional molecular biological and omic research in cancer biology and pharmacology.

    Science.gov (United States)

    Reinhold, William C

    2015-12-10

    There is currently a split within the cancer research community between traditional molecular biological hypothesis-driven and the more recent "omic" forms or research. While the molecular biological approach employs the tried and true single alteration-single response formulations of experimentation, the omic employs broad-based assay or sample collection approaches that generate large volumes of data. How to integrate the benefits of these two approaches in an efficient and productive fashion remains an outstanding issue. Ideally, one would merge the understandability, exactness, simplicity, and testability of the molecular biological approach, with the larger amounts of data, simultaneous consideration of multiple alterations, consideration of genes both of known interest along with the novel, cross-sample comparisons among cell lines and patient samples, and consideration of directed questions while simultaneously gaining exposure to the novel provided by the omic approach. While at the current time integration of the two disciplines remains problematic, attempts to do so are ongoing, and will be necessary for the understanding of the large cell line screens including the Developmental Therapeutics Program's NCI-60, the Broad Institute's Cancer Cell Line Encyclopedia, and the Wellcome Trust Sanger Institute's Cancer Genome Project, as well as the the Cancer Genome Atlas clinical samples project. Going forward there is significant benefit to be had from the integration of the molecular biological and the omic forms or research, with the desired goal being improved translational understanding and application.

  20. Group-wise ANOVA simultaneous component analysis for designed omics experiments

    NARCIS (Netherlands)

    Saccenti, Edoardo; Smilde, Age K.; Camacho, José

    2018-01-01

    Introduction: Modern omics experiments pertain not only to the measurement of many variables but also follow complex experimental designs where many factors are manipulated at the same time. This data can be conveniently analyzed using multivariate tools like ANOVA-simultaneous component analysis

  1. Genome scale models of yeast: towards standardized evaluation and consistent omic integration

    DEFF Research Database (Denmark)

    Sanchez, Benjamin J.; Nielsen, Jens

    2015-01-01

    Genome scale models (GEMs) have enabled remarkable advances in systems biology, acting as functional databases of metabolism, and as scaffolds for the contextualization of high-throughput data. In the case of Saccharomyces cerevisiae (budding yeast), several GEMs have been published and are curre......Genome scale models (GEMs) have enabled remarkable advances in systems biology, acting as functional databases of metabolism, and as scaffolds for the contextualization of high-throughput data. In the case of Saccharomyces cerevisiae (budding yeast), several GEMs have been published...... in which all levels of omics data (from gene expression to flux) have been integrated in yeast GEMs. Relevant conclusions and current challenges for both GEM evaluation and omic integration are highlighted....

  2. PRODEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP : HIGH PERFORMANCE COMPUTING WITH QCDOC AND BLUEGENE.

    Energy Technology Data Exchange (ETDEWEB)

    CHRIST,N.; DAVENPORT,J.; DENG,Y.; GARA,A.; GLIMM,J.; MAWHINNEY,R.; MCFADDEN,E.; PESKIN,A.; PULLEYBLANK,W.

    2003-03-11

    Staff of Brookhaven National Laboratory, Columbia University, IBM and the RIKEN BNL Research Center organized a one-day workshop held on February 28, 2003 at Brookhaven to promote the following goals: (1) To explore areas other than QCD applications where the QCDOC and BlueGene/L machines can be applied to good advantage, (2) To identify areas where collaboration among the sponsoring institutions can be fruitful, and (3) To expose scientists to the emerging software architecture. This workshop grew out of an informal visit last fall by BNL staff to the IBM Thomas J. Watson Research Center that resulted in a continuing dialog among participants on issues common to these two related supercomputers. The workshop was divided into three sessions, addressing the hardware and software status of each system, prospective applications, and future directions.

  3. A practical data processing workflow for multi-OMICS projects.

    Science.gov (United States)

    Kohl, Michael; Megger, Dominik A; Trippler, Martin; Meckel, Hagen; Ahrens, Maike; Bracht, Thilo; Weber, Frank; Hoffmann, Andreas-Claudius; Baba, Hideo A; Sitek, Barbara; Schlaak, Jörg F; Meyer, Helmut E; Stephan, Christian; Eisenacher, Martin

    2014-01-01

    Multi-OMICS approaches aim on the integration of quantitative data obtained for different biological molecules in order to understand their interrelation and the functioning of larger systems. This paper deals with several data integration and data processing issues that frequently occur within this context. To this end, the data processing workflow within the PROFILE project is presented, a multi-OMICS project that aims on identification of novel biomarkers and the development of new therapeutic targets for seven important liver diseases. Furthermore, a software called CrossPlatformCommander is sketched, which facilitates several steps of the proposed workflow in a semi-automatic manner. Application of the software is presented for the detection of novel biomarkers, their ranking and annotation with existing knowledge using the example of corresponding Transcriptomics and Proteomics data sets obtained from patients suffering from hepatocellular carcinoma. Additionally, a linear regression analysis of Transcriptomics vs. Proteomics data is presented and its performance assessed. It was shown, that for capturing profound relations between Transcriptomics and Proteomics data, a simple linear regression analysis is not sufficient and implementation and evaluation of alternative statistical approaches are needed. Additionally, the integration of multivariate variable selection and classification approaches is intended for further development of the software. Although this paper focuses only on the combination of data obtained from quantitative Proteomics and Transcriptomics experiments, several approaches and data integration steps are also applicable for other OMICS technologies. Keeping specific restrictions in mind the suggested workflow (or at least parts of it) may be used as a template for similar projects that make use of different high throughput techniques. This article is part of a Special Issue entitled: Computational Proteomics in the Post

  4. Integrating Omics Technologies to Study Pulmonary Physiology and Pathology at the Systems Level

    Directory of Open Access Journals (Sweden)

    Ravi Ramesh Pathak

    2014-04-01

    Full Text Available Assimilation and integration of “omics” technologies, including genomics, epigenomics, proteomics, and metabolomics has readily altered the landscape of medical research in the last decade. The vast and complex nature of omics data can only be interpreted by linking molecular information at the organismic level, forming the foundation of systems biology. Research in pulmonary biology/medicine has necessitated integration of omics, network, systems and computational biology data to differentially diagnose, interpret, and prognosticate pulmonary diseases, facilitating improvement in therapy and treatment modalities. This review describes how to leverage this emerging technology in understanding pulmonary diseases at the systems level -called a “systomic” approach. Considering the operational wholeness of cellular and organ systems, diseased genome, proteome, and the metabolome needs to be conceptualized at the systems level to understand disease pathogenesis and progression. Currently available omics technology and resources require a certain degree of training and proficiency in addition to dedicated hardware and applications, making them relatively less user friendly for the pulmonary biologist and clinicians. Herein, we discuss the various strategies, computational tools and approaches required to study pulmonary diseases at the systems level for biomedical scientists and clinical researchers.

  5. Design of a resonator for a flat-top acceleration system in the RIKEN AVF cyclotron

    International Nuclear Information System (INIS)

    Kohara, Shigeo; Miyazawa, Yoshitoshi; Kamigaito, Osamu; Goto, Akira

    1997-01-01

    A resonator for a flat-top acceleration system in the RIKEN AVF cyclotron is designed to improve the extraction efficiency and the energy spread of a beam. In order to generate the flat-top accelerating voltage on the dee, an additional resonator or a transmission line is capacitively coupled to the AVF resonator with a coupling capacitor. The flat-top accelerating voltage is obtained by the superimposition of the fundamental frequency and the fifth-harmonic-frequency voltages. Length of the additional resonator is 90 cm and capacitance of the coupling capacitor 30 pF. The frequency range of the AVF resonator is from 12 to 23 MHz. Structure and rf characteristics of the resonator designed for the flat-top acceleration system is described. (author)

  6. Chapter 3: Omics and the Future of Sustainable Biomaterials

    Science.gov (United States)

    Juliet D. Tang; Susan V. Diehl

    2014-01-01

    With global focus on the conversion of biomass into products, fuels, and energy, there is a strong need for information that will lead to new sustainable products, applications, and biotechnological advances. The omics approach to biology is a discovery-driven method that may deliver solutions to these overarching problems. It gives scientists the ability to obtain a...

  7. Omics Approach to Identify Factors Involved in Brassica Disease Resistance.

    Science.gov (United States)

    Francisco, Marta; Soengas, Pilar; Velasco, Pablo; Bhadauria, Vijai; Cartea, Maria E; Rodríguez, Victor M

    2016-01-01

    Understanding plant's defense mechanisms and their response to biotic stresses is of fundamental meaning for the development of resistant crop varieties and more productive agriculture. The Brassica genus involves a large variety of economically important species and cultivars used as vegetable source, oilseeds, forage and ornamental. Damage caused by pathogens attack affects negatively various aspects of plant growth, development, and crop productivity. Over the last few decades, advances in plant physiology, genetics, and molecular biology have greatly improved our understanding of plant responses to biotic stress conditions. In this regard, various 'omics' technologies enable qualitative and quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. In this review, we have described advances in 'omic' tools (genomics, transcriptomics, proteomics and metabolomics) in the view of conventional and modern approaches being used to elucidate the molecular mechanisms that underlie Brassica disease resistance.

  8. High spin isomer beam line at RIKEN

    Energy Technology Data Exchange (ETDEWEB)

    Kishida, T.; Ideguchi, E.; Wu, H.Y. [Institute of Physical and Chemical Research, Saitama (Japan)] [and others

    1996-12-31

    Nuclear high spin states have been the subject of extensive experimental and theoretical studies. For the production of high spin states, fusion reactions are usually used. The orbital angular momentum brought in the reaction is changed into the nuclear spin of the compound nucleus. However, the maximum induced angular momentum is limited in this mechanism by the maximum impact parameter of the fusion reaction and by the competition with fission reactions. It is, therefore, difficult to populate very high spin states, and as a result, large {gamma}-detector arrays have been developed in order to detect subtle signals from such very high spin states. The use of high spin isomers in the fusion reactions can break this limitation because the high spin isomers have their intrinsic angular momentum, which can bring the additional angular momentum without increasing the excitation energy. There are two methods to use the high spin isomers for secondary reactions: the use of the high spin isomers as a target and that as a beam. A high spin isomer target has already been developed and used for several experiments. But this method has an inevitable shortcoming that only {open_quotes}long-lived{close_quotes} isomers can be used for a target: {sup 178}Hf{sup m2} (16{sup +}) with a half-life of 31 years in the present case. By developing a high spin isomer beam, the authors can utilize various short-lived isomers with a short half-life around 1 {mu}s. The high spin isomer beam line of RIKEN Accelerator Facility is a unique apparatus in the world which provides a high spin isomer as a secondary beam. The combination of fusion-evaporation reaction and inverse kinematics are used to produce high spin isomer beams; in particular, the adoption of `inverse kinematics` is essential to use short-lived isomers as a beam.

  9. Recent advances in cowpea [ Vigna unguiculata (L.) Walp.] “omics ...

    African Journals Online (AJOL)

    After decades of research on cowpea, significant amount of omics datasets are available and useful in understanding the genetic relationship between Vigna unguiculata ssp. unguiculata and other species belonging to the same genus as well as its genetic variation. Besides, the development of genetic map allowed the ...

  10. Inflammaging and human longevity in the omics era.

    Science.gov (United States)

    Monti, Daniela; Ostan, Rita; Borelli, Vincenzo; Castellani, Gastone; Franceschi, Claudio

    2017-07-01

    Inflammaging is a recent theory of aging originally proposed in 2000 where data and conceptualizations regarding the aging of the immune system (immunosenescence) and the evolution of immune responses from invertebrates to mammals converged. This theory has received an increasing number of citations and experimental confirmations. Here we present an updated version of inflammaging focused on omics data - particularly on glycomics - collected on centenarians, semi-supercentenarians and their offspring. Accordingly, we arrived to the following conclusions: i) inflammaging has a structure where specific combinations of pro- and anti-inflammatory mediators are involved; ii) inflammaging is systemic and more complex than we previously thought, as many organs, tissues and cell types participate in producing pro- and anti-inflammatory stimuli defined "molecular garbage"; iii) inflammaging is dynamic, can be propagated locally to neighboring cells and systemically from organ to organ by circulating products and microvesicles, and amplified by chronic age-related diseases constituting a "local fire", which in turn produces additional inflammatory stimuli and molecular garbage; iv) an integrated Systems Medicine approach is urgently needed to let emerge a robust and highly informative set/combination of omics markers able to better grasp the complex molecular core of inflammaging in elderly and centenarians. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  11. Construction of new data archive system in RIKEN RI beam factory

    International Nuclear Information System (INIS)

    Komiyama, M.; Fukunishi, N.; Uchiyama, A.

    2012-01-01

    RIKEN Radioactive Isotope Beam Factory (RIBF) is a cyclotron-based next-generation radioactive beam facility. RIBF uses two types of control systems; an experimental physics and industrial control system (EPICS)-based system and a group of several non-EPICS-based systems. For each control system there is a corresponding data archiving system in operation, and in order to unify these two data archives, since October 2009 we have been developing a new archiving system. This new data archive system, named RIBF Control Data Archive System (RIBFCAS), is required, at intervals between 1 - 60 s, to collect and store more than 3000 data generated by EPICS controlled devices through EPICS input/output controllers (IOCs). In addition, RIBFCAS must be able to combine the existing non-EPICS-based systems. To fulfill these requirements, a Java-based platform has been created, and client applications are based on Adobe AIR runtime. The RIBFCAS hardware system, therefore, consists of an application server, a database server and client-PCs. Presently, we have succeeded in stably acquiring approximately 3000 data from 22 IOCs every 10 s. Moreover, incorporation of the non-EPICS-based data archive system into RIBFCAS is now in progress. (authors)

  12. NCI think tank concerning the identifiability of biospecimens and "omic" data.

    Science.gov (United States)

    Weil, Carol J; Mechanic, Leah E; Green, Tiffany; Kinsinger, Christopher; Lockhart, Nicole C; Nelson, Stefanie A; Rodriguez, Laura L; Buccini, Laura D

    2013-12-01

    On 11 and 12 June 2012, the National Cancer Institute hosted a think tank concerning the identifiability of biospecimens and "omic" data in order to explore challenges surrounding this complex and multifaceted topic. The think tank brought together 46 leaders from several fields, including cancer genomics, bioinformatics, human subject protection, patient advocacy, and commercial genetics. The first day involved presentations regarding the state of the science of reidentification; current and proposed regulatory frameworks for assessing identifiability; developments in law, industry, and biotechnology; and the expectations of patients and research participants. The second day was spent by think tank participants in small breakout groups designed to address specific subtopics under the umbrella issue of identifiability, including considerations for the development of best practices for data sharing and consent, and targeted opportunities for further empirical research. We describe the outcomes of this 2-day meeting, including two complementary themes that emerged from moderated discussions following the presentations on day 1, and ideas presented for further empirical research to discern the preferences and concerns of research participants about data sharing and individual identifiability.

  13. Ready to put metadata on the post-2015 development agenda? Linking data publications to responsible innovation and science diplomacy.

    Science.gov (United States)

    Özdemir, Vural; Kolker, Eugene; Hotez, Peter J; Mohin, Sophie; Prainsack, Barbara; Wynne, Brian; Vayena, Effy; Coşkun, Yavuz; Dereli, Türkay; Huzair, Farah; Borda-Rodriguez, Alexander; Bragazzi, Nicola Luigi; Faris, Jack; Ramesar, Raj; Wonkam, Ambroise; Dandara, Collet; Nair, Bipin; Llerena, Adrián; Kılıç, Koray; Jain, Rekha; Reddy, Panga Jaipal; Gollapalli, Kishore; Srivastava, Sanjeeva; Kickbusch, Ilona

    2014-01-01

    Metadata refer to descriptions about data or as some put it, "data about data." Metadata capture what happens on the backstage of science, on the trajectory from study conception, design, funding, implementation, and analysis to reporting. Definitions of metadata vary, but they can include the context information surrounding the practice of science, or data generated as one uses a technology, including transactional information about the user. As the pursuit of knowledge broadens in the 21(st) century from traditional "science of whats" (data) to include "science of hows" (metadata), we analyze the ways in which metadata serve as a catalyst for responsible and open innovation, and by extension, science diplomacy. In 2015, the United Nations Millennium Development Goals (MDGs) will formally come to an end. Therefore, we propose that metadata, as an ingredient of responsible innovation, can help achieve the Sustainable Development Goals (SDGs) on the post-2015 agenda. Such responsible innovation, as a collective learning process, has become a key component, for example, of the European Union's 80 billion Euro Horizon 2020 R&D Program from 2014-2020. Looking ahead, OMICS: A Journal of Integrative Biology, is launching an initiative for a multi-omics metadata checklist that is flexible yet comprehensive, and will enable more complete utilization of single and multi-omics data sets through data harmonization and greater visibility and accessibility. The generation of metadata that shed light on how omics research is carried out, by whom and under what circumstances, will create an "intervention space" for integration of science with its socio-technical context. This will go a long way to addressing responsible innovation for a fairer and more transparent society. If we believe in science, then such reflexive qualities and commitments attained by availability of omics metadata are preconditions for a robust and socially attuned science, which can then remain broadly

  14. Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of 'Omics' Data from Human Cell Cultures.

    Science.gov (United States)

    Grafström, Roland C; Nymark, Penny; Hongisto, Vesa; Spjuth, Ola; Ceder, Rebecca; Willighagen, Egon; Hardy, Barry; Kaski, Samuel; Kohonen, Pekka

    2015-11-01

    This paper outlines the work for which Roland Grafström and Pekka Kohonen were awarded the 2014 Lush Science Prize. The research activities of the Grafström laboratory have, for many years, covered cancer biology studies, as well as the development and application of toxicity-predictive in vitro models to determine chemical safety. Through the integration of in silico analyses of diverse types of genomics data (transcriptomic and proteomic), their efforts have proved to fit well into the recently-developed Adverse Outcome Pathway paradigm. Genomics analysis within state-of-the-art cancer biology research and Toxicology in the 21st Century concepts share many technological tools. A key category within the Three Rs paradigm is the Replacement of animals in toxicity testing with alternative methods, such as bioinformatics-driven analyses of data obtained from human cell cultures exposed to diverse toxicants. This work was recently expanded within the pan-European SEURAT-1 project (Safety Evaluation Ultimately Replacing Animal Testing), to replace repeat-dose toxicity testing with data-rich analyses of sophisticated cell culture models. The aims and objectives of the SEURAT project have been to guide the application, analysis, interpretation and storage of 'omics' technology-derived data within the service-oriented sub-project, ToxBank. Particularly addressing the Lush Science Prize focus on the relevance of toxicity pathways, a 'data warehouse' that is under continuous expansion, coupled with the development of novel data storage and management methods for toxicology, serve to address data integration across multiple 'omics' technologies. The prize winners' guiding principles and concepts for modern knowledge management of toxicological data are summarised. The translation of basic discovery results ranged from chemical-testing and material-testing data, to information relevant to human health and environmental safety. 2015 FRAME.

  15. Reproducibility and Transparency of Omics Research - Impacts on Human Health Risk Assessment

    Science.gov (United States)

    Omics technologies are becoming more widely used in toxicology, necessitating their consideration in human health hazard and risk assessment programs. Today, risk assessors in the United States Environmental Protection Agency’s Integrated Risk Information System (IRIS) Toxicologi...

  16. Ethnobotany, Phylogeny, and 'Omics' for Human Health and Food Security.

    Science.gov (United States)

    Garnatje, Teresa; Peñuelas, Josep; Vallès, Joan

    2017-03-01

    Here, we propose a new term, 'ethnobotanical convergence', to refer to the similar uses for plants included in the same node of a phylogeny. This phylogenetic approach, together with the 'omics' revolution, shows how combining modern technologies with traditional ethnobotanical knowledge could be used to identify potential new applications of plants. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Database Description - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us FANTOM5 Database Description General information of database Database name FANTOM5 Alternati...me: Rattus norvegicus Taxonomy ID: 10116 Taxonomy Name: Macaca mulatta Taxonomy ID: 9544 Database descriptio...l Links: Original website information Database maintenance site RIKEN Center for Life Science Technologies, ...ilable Web services Not available URL of Web services - Need for user registration Not available About This Database Database... Description Download License Update History of This Database Site Policy | Contact Us Database Description - FANTOM5 | LSDB Archive ...

  18. Global Prioritization of Disease Candidate Metabolites Based on a Multi-omics Composite Network

    Science.gov (United States)

    Yao, Qianlan; Xu, Yanjun; Yang, Haixiu; Shang, Desi; Zhang, Chunlong; Zhang, Yunpeng; Sun, Zeguo; Shi, Xinrui; Feng, Li; Han, Junwei; Su, Fei; Li, Chunquan; Li, Xia

    2015-01-01

    The identification of disease-related metabolites is important for a better understanding of metabolite pathological processes in order to improve human medicine. Metabolites, which are the terminal products of cellular regulatory process, can be affected by multi-omic processes. In this work, we propose a powerful method, MetPriCNet, to predict and prioritize disease candidate metabolites based on integrated multi-omics information. MetPriCNet prioritized candidate metabolites based on their global distance similarity with seed nodes in a composite network, which integrated multi-omics information from the genome, phenome, metabolome and interactome. After performing cross-validation on 87 phenotypes with a total of 602 metabolites, MetPriCNet achieved a high AUC value of up to 0.918. We also assessed the performance of MetPriCNet on 18 disease classes and found that 4 disease classes achieved an AUC value over 0.95. Notably, MetPriCNet can also predict disease metabolites without known disease metabolite knowledge. Some new high-risk metabolites of breast cancer were predicted, although there is a lack of known disease metabolite information. A predicted disease metabolic landscape was constructed and analyzed based on the results of MetPriCNet for 87 phenotypes to help us understand the genetic and metabolic mechanism of disease from a global view. PMID:26598063

  19. The OMICS of Sports & Space: How Genomics is Transforming Both Fields

    Science.gov (United States)

    Reeves, Katherine

    2016-01-01

    Join top 10 New York Times Bestseller “The Sports Gene” author David Epstein and NASA Twins Study investigator Christopher E. Mason, Ph.D., in the debate as old as physical competition—nature versus nurture. From personal experience, Epstein tackles the great debate and traces how far science has come in solving this timeless riddle, and how genetics has entered into the field of sports. He’s an investigative science reporter for ProPublica and longtime contributor to Sports Illustrated. Epstein will share insights into performance-enhancing drugs, the lucky genetics that separate a professional athlete from a less talented athlete, and his research into the death of a friend with Hypertrophic Cardiomyopathy (HCM).From an epigenomic viewpoint, Mason examines the benefits and risks for astronauts who face extreme spaceflight conditions and what it means for the future of human space travel. He is an associate professor in the Department of Physiology and Biophysics, The Feil Family Brain and Mind Research Institute (BMRI) & The Institute for Computational Biomedicine at Weill Cornell Medicine. He is also part of the Tri-Institutional Program on Computational Biology and a Medicine Fellow of Genomics, Ethics, and Law in the Information Society Project at Yale Law School.The study of omics shows tremendous potential in prevention, diagnosis and treatment of injuries and diseases but genetic discrimination and molecular privacy concerns are raised in both sports and space.

  20. Multi-omics analysis of inflammatory bowel disease.

    Science.gov (United States)

    Huang, Hu; Vangay, Pajau; McKinlay, Christopher E; Knights, Dan

    2014-12-01

    Crohn's disease and ulcerative colitis, known together as inflammatory bowel disease (IBD), are severe autoimmune disorders now causing gut inflammation and ulceration, among other symptoms, in up to 1 in 250 people worldwide. Incidence and prevalence of IBD have been increasing dramatically over the past several decades, although the causes for this increase are still unknown. IBD has both a complex genotype and a complex phenotype, and although it has received substantial attention from the medical research community over recent years, much of the etiology remains unexplained. Genome-wide association studies have identified a rich genetic signature of disease risk in patients with IBD, consisting of at least 163 genetic loci. Many of these loci contain genes directly involved in microbial handling, indicating that the genetic architecture of the disease has been driven by host-microbe interactions. In addition, systematic shifts in gut microbiome structure (enterotype) and function have been observed in patients with IBD. Furthermore, both the host genotype and enterotype are associated with aspects of the disease phenotype, including location of the disease. This provides strong evidence of interactions between host genotype and enterotype; however, there is a lack of published multi-omics data from IBD patients, and a lack of bioinformatics tools for modeling such systems. In this article we discuss, from a computational biologist's point of view, the potential benefits of and the challenges involved in designing and analyzing such multi-omics studies of IBD. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Validation of standard operating procedures in a multicenter retrospective study to identify -omics biomarkers for chronic low back pain.

    Directory of Open Access Journals (Sweden)

    Concetta Dagostino

    Full Text Available Chronic low back pain (CLBP is one of the most common medical conditions, ranking as the greatest contributor to global disability and accounting for huge societal costs based on the Global Burden of Disease 2010 study. Large genetic and -omics studies provide a promising avenue for the screening, development and validation of biomarkers useful for personalized diagnosis and treatment (precision medicine. Multicentre studies are needed for such an effort, and a standardized and homogeneous approach is vital for recruitment of large numbers of participants among different centres (clinical and laboratories to obtain robust and reproducible results. To date, no validated standard operating procedures (SOPs for genetic/-omics studies in chronic pain have been developed. In this study, we validated an SOP model that will be used in the multicentre (5 centres retrospective "PainOmics" study, funded by the European Community in the 7th Framework Programme, which aims to develop new biomarkers for CLBP through three different -omics approaches: genomics, glycomics and activomics. The SOPs describe the specific procedures for (1 blood collection, (2 sample processing and storage, (3 shipping details and (4 cross-check testing and validation before assays that all the centres involved in the study have to follow. Multivariate analysis revealed the absolute specificity and homogeneity of the samples collected by the five centres for all genetics, glycomics and activomics analyses. The SOPs used in our multicenter study have been validated. Hence, they could represent an innovative tool for the correct management and collection of reliable samples in other large-omics-based multicenter studies.

  2. Guiding recombinant antivenom development by omics technologies

    DEFF Research Database (Denmark)

    Laustsen, Andreas Hougaard

    2017-01-01

    directed towards the different omics technologies (particularly venomics, antivenomics, and toxicovenomics) that are being used to uncover novel animal toxins, shed light on venom complexity, and provide directions for how to determine the medical relevance of individual toxins within whole venoms. Finally......, endogenous animal proteins with toxin-neutralizing capabilities, and recombinant monoclonal antibodies. Harnessing either of these approaches, antivenom development may benefit from an in-depth understanding of venom compositions and the medical importance of individual venom toxins. Focus is thus also......, techniques for assessing antivenom specificity and cross-reactivity are reviewed, with special focus on antivenomics and high-density peptide microarray technology....

  3. Mildew-omics: How global analyses aid the understanding of life and evolution of powdery mildews

    Directory of Open Access Journals (Sweden)

    Laurence Veronique Bindschedler

    2016-02-01

    Full Text Available The common powdery mildew plant diseases are caused by ascomycete fungi of the order Erysiphales. Their characteristic life style as obligate biotrophs renders functional analyses in these species challenging, mainly because of experimental constraints to genetic manipulation. Global large-scale (-omics approaches are thus particularly valuable and insightful for the characterisation of the life and evolution of powdery mildews. Here we review the knowledge obtained so far from genomic, transcriptomic and proteomic studies in these fungi. We consider current limitations and challenges regarding these surveys and provide an outlook on desired future investigations on the basis of the various –omics technologies.

  4. First results from the new RIKEN superconducting electron cyclotron resonance ion source (invited).

    Science.gov (United States)

    Nakagawa, T; Higurashi, Y; Ohnishi, J; Aihara, T; Tamura, M; Uchiyama, A; Okuno, H; Kusaka, K; Kidera, M; Ikezawa, E; Fujimaki, M; Sato, Y; Watanabe, Y; Komiyama, M; Kase, M; Goto, A; Kamigaito, O; Yano, Y

    2010-02-01

    The next generation heavy ion accelerator facility, such as the RIKEN radio isotope (RI) beam factory, requires an intense beam of high charged heavy ions. In the past decade, performance of the electron cyclotron resonance (ECR) ion sources has been dramatically improved with increasing the magnetic field and rf frequency to enhance the density and confinement time of plasma. Furthermore, the effects of the key parameters (magnetic field configuration, gas pressure, etc.) on the ECR plasma have been revealed. Such basic studies give us how to optimize the ion source structure. Based on these studies and modern superconducting (SC) technology, we successfully constructed the new 28 GHz SC-ECRIS, which has a flexible magnetic field configuration to enlarge the ECR zone and to optimize the field gradient at ECR point. Using it, we investigated the effect of ECR zone size, magnetic field configuration, and biased disk on the beam intensity of the highly charged heavy ions with 18 GHz microwaves. In this article, we present the structure of the ion source and first experimental results with 18 GHz microwave in detail.

  5. Science and Biotechnology plant will be ready to ensure food the world population 2050?

    International Nuclear Information System (INIS)

    Stanca, Michele A.

    2015-01-01

    The new challenges of modern agriculture to feed the world will rely more and more on science and technological innovation, particularly that derived from 'omics' disciplines, and the speed with which these new techniques will reach the farm. [it

  6. Incorporation of omics analyses into artificial gravity research for space exploration countermeasure development.

    Science.gov (United States)

    Schmidt, Michael A; Goodwin, Thomas J; Pelligra, Ralph

    The next major steps in human spaceflight include flyby, orbital, and landing missions to the Moon, Mars, and near earth asteroids. The first crewed deep space mission is expected to launch in 2022, which affords less than 7 years to address the complex question of whether and how to apply artificial gravity to counter the effects of prolonged weightlessness. Various phenotypic changes are demonstrated during artificial gravity experiments. However, the molecular dynamics (genotype and molecular phenotypes) that underlie these morphological, physiological, and behavioral phenotypes are far more complex than previously understood. Thus, targeted molecular assessment of subjects under various G conditions can be expected to miss important patterns of molecular variance that inform the more general phenotypes typically being measured. Use of omics methods can help detect changes across broad molecular networks, as various G-loading paradigms are applied. This will be useful in detecting off-target, or unanticipated effects of the different gravity paradigms applied to humans or animals. Insights gained from these approaches may eventually be used to inform countermeasure development or refine the deployment of existing countermeasures. This convergence of the omics and artificial gravity research communities may be critical if we are to develop the proper artificial gravity solutions under the severely compressed timelines currently established. Thus, the omics community may offer a unique ability to accelerate discovery, provide new insights, and benefit deep space missions in ways that have not been previously considered.

  7. Research from the NASA Twins Study and Omics in Support of Mars Missions

    Science.gov (United States)

    Kundrot, C.; Shelhamer, M.; Scott, G.

    2015-01-01

    The NASA Twins Study, NASA's first foray into integrated omic studies in humans, illustrates how an integrated omics approach can be brought to bear on the challenges to human health and performance on a Mars mission. The NASA Twins Study involves US Astronaut Scott Kelly and his identical twin brother, Mark Kelly, a retired US Astronaut. No other opportunity to study a twin pair for a prolonged period with one subject in space and one on the ground is available for the foreseeable future. A team of 10 principal investigators are conducting the Twins Study, examining a very broad range of biological functions including the genome, epigenome, transcriptome, proteome, metabolome, gut microbiome, immunological response to vaccinations, indicators of atherosclerosis, physiological fluid shifts, and cognition. A novel aspect of the study is the integrated study of molecular, physiological, cognitive, and microbiological properties. Major sample and data collection from both subjects for this study began approximately six months before Scott Kelly's one year mission on the ISS, continue while Scott Kelly is in flight and will conclude approximately six months after his return to Earth. Mark Kelly will remain on Earth during this study, in a lifestyle unconstrained by this study, thereby providing a measure of normal variation in the properties being studied. An overview of initial results and the future plans will be described as well as the technological and ethical issues raised for spaceflight studies involving omics.

  8. OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space.

    Science.gov (United States)

    Zhou, Guangyan; Xia, Jianguo

    2018-06-07

    Biological networks play increasingly important roles in omics data integration and systems biology. Over the past decade, many excellent tools have been developed to support creation, analysis and visualization of biological networks. However, important limitations remain: most tools are standalone programs, the majority of them focus on protein-protein interaction (PPI) or metabolic networks, and visualizations often suffer from 'hairball' effects when networks become large. To help address these limitations, we developed OmicsNet - a novel web-based tool that allows users to easily create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space. Users can upload one or multiple lists of molecules of interest (genes/proteins, microRNAs, transcription factors or metabolites) to create and merge different types of biological networks. The 3D network visualization system was implemented using the powerful Web Graphics Library (WebGL) technology that works natively in most major browsers. OmicsNet supports force-directed layout, multi-layered perspective layout, as well as spherical layout to help visualize and navigate complex networks. A rich set of functions have been implemented to allow users to perform coloring, shading, topology analysis, and enrichment analysis. OmicsNet is freely available at http://www.omicsnet.ca.

  9. Onco-proteogenomics: Multi-omics level data integration for accurate phenotype prediction.

    Science.gov (United States)

    Dimitrakopoulos, Lampros; Prassas, Ioannis; Diamandis, Eleftherios P; Charames, George S

    2017-09-01

    The overall goal of translational oncology is to identify molecular alterations indicative of cancer or of responsiveness to specific therapeutic regimens. While next-generation sequencing has played a pioneering role in this quest, the latest advances in proteomic technologies promise to provide a holistic approach to the further elucidation of tumor biology. Genetic information may be written in DNA and flow from DNA to RNA to protein, according to the central dogma of molecular biology, but the observed phenotype is dictated predominantly by the DNA protein coding region-derived proteotype. Proteomics holds the potential to bridge the gap between genotype and phenotype, because the powerful analytical tool of mass spectrometry has reached a point of maturity to serve this purpose effectively. This integration of "omics" data has given birth to the novel field of onco-proteogenomics, which has much to offer to precision medicine and personalized patient management. Here, we review briefly how each "omics" technology has individually contributed to cancer research, discuss technological and computational advances that have contributed to the realization of onco-proteogenomics, and summarize current and future translational applications.

  10. The Perseus computational platform for comprehensive analysis of (prote)omics data.

    Science.gov (United States)

    Tyanova, Stefka; Temu, Tikira; Sinitcyn, Pavel; Carlson, Arthur; Hein, Marco Y; Geiger, Tamar; Mann, Matthias; Cox, Jürgen

    2016-09-01

    A main bottleneck in proteomics is the downstream biological analysis of highly multivariate quantitative protein abundance data generated using mass-spectrometry-based analysis. We developed the Perseus software platform (http://www.perseus-framework.org) to support biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiple-hypothesis testing. A machine learning module supports the classification and validation of patient groups for diagnosis and prognosis, and it also detects predictive protein signatures. Central to Perseus is a user-friendly, interactive workflow environment that provides complete documentation of computational methods used in a publication. All activities in Perseus are realized as plugins, and users can extend the software by programming their own, which can be shared through a plugin store. We anticipate that Perseus's arsenal of algorithms and its intuitive usability will empower interdisciplinary analysis of complex large data sets.

  11. Computational Omics Pre-Awardees | Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) is pleased to announce the pre-awardees of the Computational Omics solicitation. Working with NVIDIA Foundation's Compute the Cure initiative and Leidos Biomedical Research Inc., the NCI, through this solicitation, seeks to leverage computational efforts to provide tools for the mining and interpretation of large-scale publicly available ‘omics’ datasets.

  12. An integrative omics perspective for the analysis of chemical signals in ecological interactions.

    Science.gov (United States)

    Brunetti, A E; Carnevale Neto, F; Vera, M C; Taboada, C; Pavarini, D P; Bauermeister, A; Lopes, N P

    2018-03-05

    All living organisms emit, detect, and respond to chemical stimuli, thus creating an almost limitless number of interactions by means of chemical signals. Technological and intellectual advances in the last two decades have enabled chemical signals analyses at several molecular levels, including gene expression, molecular diversity, and receptor affinity. These advances have also deepened our understanding of nature to encompass interactions at multiple organism levels across different taxa. This tutorial review describes the most recent analytical developments in 'omics' technologies (i.e., genomics, transcriptomics, proteomics, and metabolomics) and provide recent examples of its application in studies of chemical signals. We highlight how studies have integrated an enormous amount of information generated from different omics disciplines into one publicly available platform. In addition, we stress the importance of considering different signal modalities and an evolutionary perspective to establish a comprehensive understanding of chemical communication.

  13. Linking Ecological, Environmental and Biogeochemical Data with Multi'omics Analysis

    Science.gov (United States)

    Hasler-Sheetal, H.; Castorani, M. C.; Fragner, L.; Zeng, Y.; Holmer, M.; Glud, R. N.; Weckwerth, W.; Canfield, D. E.

    2016-02-01

    The integrated analysis of multi'omics and environmental data provides a holistic understanding of biological processes and has been proven to be challenging. Here we present our research concept for conducting multi-omics experiments and linking them to environmental data. Hypoxia, reduced light availability and species interaction - all amplified by global warming - cause a global decline of seagrasses. Metabolic mechanisms for coping with these global threats are largely unknown and multi'omics approaches can be an important approach for generating this insight. We applied GC, LC-qTOF-MS and bioinformatics to investigate the effects of environmental pressure on metabolites present in seagrasses. In a first experiment we assessed the metabolomics response of the seagrass Zostera marina towards anoxia and showed that photosynthetically derived oxygen could satisfy the oxygen demand in the leaves. But accumulation of fermentation products in the roots showed that the rhizosphere was under anoxic stress. In contrast nocturnal anoxia caused a biphasic shift in the metabolome of roots and leaves. This nocturnal reprogramming of the metabolome under anoxia indicates a mitigation mechanism to avoid the toxic effects. A pathway enrichment analysis proposes the alanine shunt, the GABA shunt and the 2-oxoglutarate shunt as such mitigation mechanisms that alleviate pyruvate levels and lead to carbon and nitrogen storage during anoxia. In a second experiment, varying light exposure and species interaction of Z. marina with the blue mussel Mytilus edulis - a co-occurring species in seagrass systems - resulted in treatment specific metabolic fingerprints in seagrass. Light modified the metabolic fingerprint expressed in Z. marina to the presence of mussels, indicating varying physiological responses to mussels in normal and low light regimes. Multivariate data-analysis indicated light exposure as main driver (45%) and mussel presence as minor driver (13%) for the metabolic

  14. Framework for the quantitative weight-of-evidence analysis of 'omics data for regulatory purposes.

    Science.gov (United States)

    Bridges, Jim; Sauer, Ursula G; Buesen, Roland; Deferme, Lize; Tollefsen, Knut E; Tralau, Tewes; van Ravenzwaay, Ben; Poole, Alan; Pemberton, Mark

    2017-12-01

    A framework for the quantitative weight-of-evidence (QWoE) analysis of 'omics data for regulatory purposes is presented. The QWoE framework encompasses seven steps to evaluate 'omics data (also together with non-'omics data): (1) Hypothesis formulation, identification and weighting of lines of evidence (LoEs). LoEs conjoin different (types of) studies that are used to critically test the hypothesis. As an essential component of the QWoE framework, step 1 includes the development of templates for scoring sheets that predefine scoring criteria with scores of 0-4 to enable a quantitative determination of study quality and data relevance; (2) literature searches and categorisation of studies into the pre-defined LoEs; (3) and (4) quantitative assessment of study quality and data relevance using the respective pre-defined scoring sheets for each study; (5) evaluation of LoE-specific strength of evidence based upon the study quality and study relevance scores of the studies conjoined in the respective LoE; (6) integration of the strength of evidence from the individual LoEs to determine the overall strength of evidence; (7) characterisation of uncertainties and conclusion on the QWoE. To put the QWoE framework in practice, case studies are recommended to confirm the relevance of its different steps, or to adapt them as necessary. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  15. PROCEEDINGS FROM RIKEN-BNL RESEARCH CENTER WORKSHOP: PARITY-VIOLATING SPIN ASYMMETRIES AT RHIC

    International Nuclear Information System (INIS)

    VOGELSANG, W.; PERDEKAMP, M.; SURROW, B.

    2007-01-01

    The RHIC spin program is now fully underway. Several runs have been successfully completed and are producing exciting first results. Luminosity and polarization have improved remarkably and promising advances toward the higher RHIC energy of √s = 500 GeV have been made. At this energy in particular, it will become possible to perform measurements of parity-violating spin asymmetries. Parity violation occurs in weak interactions, and in combination with the unique polarization capabilities at RHIC fascinating new opportunities arise. In particular, parity-violating single- and double-spin asymmetries give new insights into nucleon structure by allowing probes of up and down sea and anti-quark polarizations. Such measurements at RHIC are a DOE performance milestone for the year 2013 and are also supported by a very large effort from RIKEN. With transverse polarization, charged-current interactions may be sensitive to the Sivers effect. Parity-violating effects at RHIC have been proposed even as probes of physics beyond the Standard Model. With the era of measurements of parity-violating spin asymmetries at RHIC now rapidly approaching, we had proposed a small workshop that would bring together the main experts in both theory and experiment. We are very happy that this worked out. The whole workshop contained 17 formal talks, both experiment (10) and theory (7), and many fruitful discussions. The physics motivations for, the planned measurements were reviewed first. The RHIC machine prospects regarding polarized 500 GeV running were discussed, as well as the plans by the RHIC experiments for the vital upgrades of their detectors needed for the W physics program. We also had several talks on the topic of ''semi-inclusive deep-inelastic scattering'', which provides different access to related physics observables. On the theory side, new calculations were presented, for example in terms of QCD all-order resummations of perturbation theory. Also, new observables, such

  16. Chapter 3: Omics Advances of Biosynthetic Pathways of Isoprenoid Production in Microalgae

    Energy Technology Data Exchange (ETDEWEB)

    Paniagua-Michel, J.; Subramanian, Venkataramanan

    2017-01-01

    In this chapter, the current status of microalgal isoprenoids and the role of omics technologies, or otherwise specified, in bioproducts optimization and applications are reviewed. Emphasis is focused in the metabolic pathways of microalgae involved in the production of commercially important products, namely, hydrocarbons and biofuels, nutraceuticals, and pharmaceuticals.

  17. 'Omics' biomarkers associated with chronic low back pain: protocol of a retrospective longitudinal study.

    Science.gov (United States)

    Allegri, Massimo; De Gregori, Manuela; Minella, Cristina E; Klersy, Catherine; Wang, Wei; Sim, Moira; Gieger, Christian; Manz, Judith; Pemberton, Iain K; MacDougall, Jane; Williams, Frances Mk; Van Zundert, Jan; Buyse, Klaas; Lauc, Gordan; Gudelj, Ivan; Primorac, Dragan; Skelin, Andrea; Aulchenko, Yurii S; Karssen, Lennart C; Kapural, Leonardo; Rauck, Richard; Fanelli, Guido

    2016-10-19

    Chronic low back pain (CLBP) produces considerable direct costs as well as indirect burdens for society, industry and health systems. CLBP is characterised by heterogeneity, inclusion of several pain syndromes, different underlying molecular pathologies and interaction with psychosocial factors that leads to a range of clinical manifestations. There is still much to understand in the underlying pathological processes and the non-psychosocial factors which account for differences in outcomes. Biomarkers that may be objectively used for diagnosis and personalised, targeted and cost-effective treatment are still lacking. Therefore, any data that may be obtained at the '-omics' level (glycomics, Activomics and genome-wide association studies-GWAS) may be helpful to use as dynamic biomarkers for elucidating CLBP pathogenesis and may ultimately provide prognostic information too. By means of a retrospective, observational, case-cohort, multicentre study, we aim to investigate new promising biomarkers potentially able to solve some of the issues related to CLBP. The study follows a two-phase, 1:2 case-control model. A total of 12 000 individuals (4000 cases and 8000 controls) will be enrolled; clinical data will be registered, with particular attention to pain characteristics and outcomes of pain treatments. Blood samples will be collected to perform -omics studies. The primary objective is to recognise genetic variants associated with CLBP; secondary objectives are to study glycomics and Activomics profiles associated with CLBP. The study is part of the PainOMICS project funded by European Community in the Seventh Framework Programme. The study has been approved from competent ethical bodies and copies of approvals were provided to the European Commission before starting the study. Results of the study will be reviewed by the Scientific Board and Ethical Committee of the PainOMICS Consortium. The scientific results will be disseminated through peer-reviewed journals

  18. Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

    Directory of Open Access Journals (Sweden)

    Muneer A. Malla

    2018-06-01

    Full Text Available Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

  19. Biomarkers in neonatology: the new "omics" of bronchopulmonary dysplasia.

    Science.gov (United States)

    Piersigilli, Fiammetta; Bhandari, Vineet

    2016-01-01

    Bronchopulmonary dysplasia (BPD) is a complex disorder resulting from gene-environmental interactions. An improved understanding of the pathogenesis of this most common chronic lung disease in infants has been made by utilizing animal models and correlating with human data. Currently, while some (vitamin A, caffeine) pharmacotherapeutic options are being utilized to ameliorate this condition, there is still no specific or effective treatment for BPD. It would be helpful for prognostication and targeted potential novel therapeutic strategies to identify those babies accurately who are at risk for developing this disease. A reliable biomarker would have the capacity to be detected in the initial phase of the disease, to allow early interventions to avoid or minimize the detrimental effects of the disease. This review will focus on human studies performed with the "omic" techniques, specifically genomics, epigenomics, microbiomics, transciptomics, proteomics and metabolomics, and summarize the information available in the literature, as it pertains to biomarker identification for BPD. Using "omics" technologies, investigators have reported markers that have the potential to be used as biomarkers of BPD: SPOCK2, VEGF -624C > G, VEGF -460T > C, mast cells specific markers, miR-219 pathway, miR-152, -30a-3p, -133b, -206, -7, lactate, taurine, trimethylamine-N-oxide, gluconate, myoinositol and alterations in surfactant lipid profile.

  20. PhenoLink - a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains

    Directory of Open Access Journals (Sweden)

    Bayjanov Jumamurat R

    2012-05-01

    Full Text Available Abstract Background Linking phenotypes to high-throughput molecular biology information generated by ~omics technologies allows revealing cellular mechanisms underlying an organism's phenotype. ~Omics datasets are often very large and noisy with many features (e.g., genes, metabolite abundances. Thus, associating phenotypes to ~omics data requires an approach that is robust to noise and can handle large and diverse data sets. Results We developed a web-tool PhenoLink (http://bamics2.cmbi.ru.nl/websoftware/phenolink/ that links phenotype to ~omics data sets using well-established as well new techniques. PhenoLink imputes missing values and preprocesses input data (i to decrease inherent noise in the data and (ii to counterbalance pitfalls of the Random Forest algorithm, on which feature (e.g., gene selection is based. Preprocessed data is used in feature (e.g., gene selection to identify relations to phenotypes. We applied PhenoLink to identify gene-phenotype relations based on the presence/absence of 2847 genes in 42 Lactobacillus plantarum strains and phenotypic measurements of these strains in several experimental conditions, including growth on sugars and nitrogen-dioxide production. Genes were ranked based on their importance (predictive value to correctly predict the phenotype of a given strain. In addition to known gene to phenotype relations we also found novel relations. Conclusions PhenoLink is an easily accessible web-tool to facilitate identifying relations from large and often noisy phenotype and ~omics datasets. Visualization of links to phenotypes offered in PhenoLink allows prioritizing links, finding relations between features, finding relations between phenotypes, and identifying outliers in phenotype data. PhenoLink can be used to uncover phenotype links to a multitude of ~omics data, e.g., gene presence/absence (determined by e.g.: CGH or next-generation sequencing, gene expression (determined by e.g.: microarrays or RNA

  1. Stemcell Information: SKIP000144 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Makoto Otsu --Huan-Ting Lin 大津 真--Huan-Ting Lin University of Tokyo, Institute of Medical Science--U...niversity of Tokyo, Institute of Medical Science 東京大学医科学研究所--東京大学医科学研究所 Universit...y of Tokyo, Institute of Medical Science 東京大学医科学研究所 Makoto Otsu 大津 真 Not Available Riken BRC 理研BRC http://www.brc.riken.jp/lab/cell/english/patient_specific_ips.shtml ...

  2. Stemcell Information: SKIP000145 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Makoto Otsu --Huan-Ting Lin 大津 真--Huan-Ting Lin University of Tokyo, Institute of Medical Science--Un...iversity of Tokyo, Institute of Medical Science 東京大学医科学研究所--東京大学医科学研究所 University... of Tokyo, Institute of Medical Science 東京大学医科学研究所 Makoto Otsu 大津 真 Not Available Riken BRC 理研BRC http://www.brc.riken.jp/lab/cell/english/patient_specific_ips.shtml ...

  3. Mass spectrometry in life science research.

    Science.gov (United States)

    Lehr, Stefan; Markgraf, Daniel

    2016-12-01

    Investigating complex signatures of biomolecules by mass spectrometry approaches has become indispensable in molecular life science research. Nowadays, various mass spectrometry-based omics technologies are available to monitor qualitative and quantitative changes within hundreds or thousands of biological active components, including proteins/peptides, lipids and metabolites. These comprehensive investigations have the potential to decipher the pathophysiology of disease development at a molecular level and to monitor the individual response of pharmacological treatment or lifestyle intervention.

  4. The RIKEN gas-filled recoil separator and a possible new approach to superheavy elements by the (HI, αxn) reaction

    International Nuclear Information System (INIS)

    Nomura, T.

    1990-10-01

    The (HI, αxn) reaction, in which precompound α particle emission takes place, is shown to occur significantly even near the Coulomb barrier. Because the α emission can efficiently cool down a highly excited nucleus both in energy and angular momentum, it is considered to be very effective for production of heavy elements like SHE. However, the angular distributions of residual nuclei produced in this reaction are side-peaked, requiring a recoil-type separator with large angular acceptance when it is applied for collection of the relevant nuclei. A brief description is given about a gas-filled separator recently constructed at RIKEN, which meets the above requirement. (author)

  5. PROCEEDINGS OF RIKEN/BNL RESEARCH CENTER WORKSHOP FUTURE TRANSVERSITY MEASUREMENTS (VOLUME 29)

    International Nuclear Information System (INIS)

    Boer, D.; Grosse Perdekamp, M.

    2001-01-01

    The RIKEN-BNL Research Center workshop on ''Future Transversity Measurements'' was held at BNL from September 18-20, 2000. The main goal of the workshop was to explore future measurements of transversity distributions. This issue is of importance to the RHIC experiments, which will study polarized proton-proton collisions with great precision. One of the workshop's goals was to enhance interactions between the DIS community at HERA and the spin community at RHIC in this field. The workshop has been well received by the participants; the number of 69 registered participants demonstrates broad interest in the workshop's topics. The program contained 35 talks and there was ample time for lively discussions. The program covered all recent work in the field and in addition some very elucidating educational talks were given. At the workshop the present status of the field was discussed and it has succeeded in stimulating new experimental and theoretical studies (e.g. model calculations for interference fragmentation functions (IFF), IFF analysis at DELPHI). It also functioned to focus attention on the open questions that need to be resolved for near future experiments. In general, the conclusions were optimistic, i.e. measuring the transversity functions seems to be possible, although some new experimental hurdles will have to be taken

  6. Proceedings of RIKEN BNL Research Center Workshop: The Physics of W and Z Bosons

    Energy Technology Data Exchange (ETDEWEB)

    Dawson, S.; Okada, K.; Patwa, A.; Qiu, J.; Surrow, B.

    2010-06-24

    A two-day workshop on 'The Physics of Wand Z Bosons' Was held at the RIKEN BNL Research Center at Brookhaven National Laboratory on June 24-25, 2010. With the recent release of the first measurement of W bosons in proton-proton collisions at RHIC and the first observation of W events at the LHC, the workshop was a timely opportunity to bring together experts from both the high energy particle and nuclear physics communities to share their ideas and expertise on the physics of Wand Z bosons, with the aim of fully exploring the potential of the W/Z physics programs at RHIC and the LHC. The focus was on the production and measurement of W/Z bosons in both polarized and unpolarized proton-proton collisions, and the role of W/Z production in probing the parton flavor and helicity structure of the colliding proton and in the search for new physics. There were lively discussions about the potential and future prospects of W/Z programs at RHIC, Tevatron, and the LHC.

  7. Insect Gallers and Their Plant Hosts: From Omics Data to Systems Biology

    Directory of Open Access Journals (Sweden)

    Caryn N. Oates

    2016-11-01

    Full Text Available Gall-inducing insects are capable of exerting a high level of control over their hosts’ cellular machinery to the extent that the plant’s development, metabolism, chemistry, and physiology are all altered in favour of the insect. Many gallers are devastating pests in global agriculture and the limited understanding of their relationship with their hosts prevents the development of robust management strategies. Omics technologies are proving to be important tools in elucidating the mechanisms involved in the interaction as they facilitate analysis of plant hosts and insect effectors for which little or no prior knowledge exists. In this review, we examine the mechanisms behind insect gall development using evidence from omics-level approaches. The secretion of effector proteins and induced phytohormonal imbalances are highlighted as likely mechanisms involved in gall development. However, understanding how these components function within the system is far from complete and a number of questions need to be answered before this information can be used in the development of strategies to engineer or breed plants with enhanced resistance.

  8. 'Omics' Approaches to Understanding Interstitial Cystitis/Painful Bladder Syndrome/Bladder Pain Syndrome

    Directory of Open Access Journals (Sweden)

    Sungyong You

    2012-12-01

    Full Text Available Recent efforts in the generation of large genomics, transcriptomics, proteomics, metabolomics and other types of 'omics' data sets have provided an unprecedentedly detailed view of certain diseases, however to date most of this literature has been focused on malignancy and other lethal pathological conditions. Very little intensive work on global profiles has been performed to understand the molecular mechanism of interstitial cystitis/painful bladder syndrome/bladder pain syndrome (IC/PBS/BPS, a chronic lower urinary tract disorder characterized by pelvic pain, urinary urgency and frequency, which can lead to long lasting adverse effects on quality of life. A lack of understanding of molecular mechanism has been a challenge and dilemma for diagnosis and treatment, and has also led to a delay in basic and translational research focused on biomarker and drug discovery, clinical therapy, and preventive strategies against IC/PBS/BPS. This review describes the current state of 'omics' studies and available data sets relevant to IC/PBS/BPS, and presents opportunities for new research directed at understanding the pathogenesis of this complex condition.

  9. A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis

    Directory of Open Access Journals (Sweden)

    Jean-Guillaume Emond-Rheault

    2017-06-01

    Full Text Available The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS, at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how Salmonella evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance.

  10. Culturomics: A New Kid on the Block of OMICS to Enable Personalized Medicine.

    Science.gov (United States)

    Kambouris, Manousos E; Pavlidis, Cristiana; Skoufas, Efthymios; Arabatzis, Michael; Kantzanou, Maria; Velegraki, Aristea; Patrinos, George P

    2018-02-01

    This innovation analysis highlights the underestimated and versatile potential of the new field of culturomics and examines its relation to other OMICS system sciences such as infectiomics, metabolomics, phenomics, and pharmacomicrobiomics. The advent of molecular biology, followed by the emergence of various disciplines of the genomics, and most importantly metagenomics, brought about the sharp decline of conventional microbiology methods. Emergence of culturomics has a natural synergy with therapeutic and clinical genomic approaches so as to realize personalized medicine. Notably, the concept of culturomics expands on that of phenomics and allows a reintroduction of the culture-based phenotypic characterization into the 21st century research repertoire, bolstered by robust technology for automated and massive execution, but its potential is largely unappreciated at present; the few available references show unenthusiastic pursuit and in narrow applications. This has not to be so: depending on the specific brand of culturomics, the scope of applications may extend to medicine, agriculture, environmental sciences, pharmacomicrobiomics, and biotechnology innovation. Moreover, culturomics may produce Big Data. This calls for a new generation of data scientists and innovative ways of harnessing and valorizing Big Data beyond classical genomics. Much more detailed and objective classification and identification of microbiota may soon be at hand through culturomics, thus enabling precision diagnosis toward truly personalized medicine. Culturomics may both widen the scope of microbiology and improve its contributions to diagnostics and personalized medicine, characterizing microbes and determining their associations with health and disease dynamics.

  11. Guiding recombinant antivenom development by omics technologies

    DEFF Research Database (Denmark)

    Laustsen, Andreas Hougaard

    2017-01-01

    , endogenous animal proteins with toxin-neutralizing capabilities, and recombinant monoclonal antibodies. Harnessing either of these approaches, antivenom development may benefit from an in-depth understanding of venom compositions and the medical importance of individual venom toxins. Focus is thus also...... directed towards the different omics technologies (particularly venomics, antivenomics, and toxicovenomics) that are being used to uncover novel animal toxins, shed light on venom complexity, and provide directions for how to determine the medical relevance of individual toxins within whole venoms. Finally......In this review, the different approaches that have been employed with the aim of developing novel antivenoms against animal envenomings are presented and discussed. Reported efforts have focused on the use of innovative immunization strategies, small molecule inhibitors against enzymatic toxins...

  12. The Omics Dashboard for interactive exploration of gene-expression data.

    Science.gov (United States)

    Paley, Suzanne; Parker, Karen; Spaulding, Aaron; Tomb, Jean-Francois; O'Maille, Paul; Karp, Peter D

    2017-12-01

    The Omics Dashboard is a software tool for interactive exploration and analysis of gene-expression datasets. The Omics Dashboard is organized as a hierarchy of cellular systems. At the highest level of the hierarchy the Dashboard contains graphical panels depicting systems such as biosynthesis, energy metabolism, regulation and central dogma. Each of those panels contains a series of X-Y plots depicting expression levels of subsystems of that panel, e.g. subsystems within the central dogma panel include transcription, translation and protein maturation and folding. The Dashboard presents a visual read-out of the expression status of cellular systems to facilitate a rapid top-down user survey of how all cellular systems are responding to a given stimulus, and to enable the user to quickly view the responses of genes within specific systems of interest. Although the Dashboard is complementary to traditional statistical methods for analysis of gene-expression data, we show how it can detect changes in gene expression that statistical techniques may overlook. We present the capabilities of the Dashboard using two case studies: the analysis of lipid production for the marine alga Thalassiosira pseudonana, and an investigation of a shift from anaerobic to aerobic growth for the bacterium Escherichia coli. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Analysis of metabolomic data: tools, current strategies and future challenges for omics data integration.

    Science.gov (United States)

    Cambiaghi, Alice; Ferrario, Manuela; Masseroli, Marco

    2017-05-01

    Metabolomics is a rapidly growing field consisting of the analysis of a large number of metabolites at a system scale. The two major goals of metabolomics are the identification of the metabolites characterizing each organism state and the measurement of their dynamics under different situations (e.g. pathological conditions, environmental factors). Knowledge about metabolites is crucial for the understanding of most cellular phenomena, but this information alone is not sufficient to gain a comprehensive view of all the biological processes involved. Integrated approaches combining metabolomics with transcriptomics and proteomics are thus required to obtain much deeper insights than any of these techniques alone. Although this information is available, multilevel integration of different 'omics' data is still a challenge. The handling, processing, analysis and integration of these data require specialized mathematical, statistical and bioinformatics tools, and several technical problems hampering a rapid progress in the field exist. Here, we review four main tools for number of users or provided features (MetaCoreTM, MetaboAnalyst, InCroMAP and 3Omics) out of the several available for metabolomic data analysis and integration with other 'omics' data, highlighting their strong and weak aspects; a number of related issues affecting data analysis and integration are also identified and discussed. Overall, we provide an objective description of how some of the main currently available software packages work, which may help the experimental practitioner in the choice of a robust pipeline for metabolomic data analysis and integration. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  14. Application of OMICS technologies in occupational and environmental health research; current status and projections.

    NARCIS (Netherlands)

    Vlaanderen, J.J.; Moore, L.E.; Smith, M.T.; Lan, Q.; Zhang, L.; Skibola, C.F.; Rothman, N.; Vermeulen, R.

    2010-01-01

    OMICS technologies are relatively new biomarker discovery tools that can be applied to study large sets of biological molecules. Their application in human observational studies (HOS) has become feasible in recent years due to a spectacular increase in the sensitivity, resolution and throughput of

  15. Redundancy control in pathway databases (ReCiPa): an application for improving gene-set enrichment analysis in Omics studies and "Big data" biology.

    Science.gov (United States)

    Vivar, Juan C; Pemu, Priscilla; McPherson, Ruth; Ghosh, Sujoy

    2013-08-01

    Abstract Unparalleled technological advances have fueled an explosive growth in the scope and scale of biological data and have propelled life sciences into the realm of "Big Data" that cannot be managed or analyzed by conventional approaches. Big Data in the life sciences are driven primarily via a diverse collection of 'omics'-based technologies, including genomics, proteomics, metabolomics, transcriptomics, metagenomics, and lipidomics. Gene-set enrichment analysis is a powerful approach for interrogating large 'omics' datasets, leading to the identification of biological mechanisms associated with observed outcomes. While several factors influence the results from such analysis, the impact from the contents of pathway databases is often under-appreciated. Pathway databases often contain variously named pathways that overlap with one another to varying degrees. Ignoring such redundancies during pathway analysis can lead to the designation of several pathways as being significant due to high content-similarity, rather than truly independent biological mechanisms. Statistically, such dependencies also result in correlated p values and overdispersion, leading to biased results. We investigated the level of redundancies in multiple pathway databases and observed large discrepancies in the nature and extent of pathway overlap. This prompted us to develop the application, ReCiPa (Redundancy Control in Pathway Databases), to control redundancies in pathway databases based on user-defined thresholds. Analysis of genomic and genetic datasets, using ReCiPa-generated overlap-controlled versions of KEGG and Reactome pathways, led to a reduction in redundancy among the top-scoring gene-sets and allowed for the inclusion of additional gene-sets representing possibly novel biological mechanisms. Using obesity as an example, bioinformatic analysis further demonstrated that gene-sets identified from overlap-controlled pathway databases show stronger evidence of prior association

  16. Bioinformatics and biomarker discovery "Omic" data analysis for personalized medicine

    CERN Document Server

    Azuaje, Francisco

    2010-01-01

    This book is designed to introduce biologists, clinicians and computational researchers to fundamental data analysis principles, techniques and tools for supporting the discovery of biomarkers and the implementation of diagnostic/prognostic systems. The focus of the book is on how fundamental statistical and data mining approaches can support biomarker discovery and evaluation, emphasising applications based on different types of "omic" data. The book also discusses design factors, requirements and techniques for disease screening, diagnostic and prognostic applications. Readers are provided w

  17. PROCEEDINGS OF RIKEN/BNL RESEARCH CENTER WORKSHOP FUTURE TRANSVERSITY MEASUREMENTS (VOLUME 29).

    Energy Technology Data Exchange (ETDEWEB)

    Boer, D.; Grosse Perdekamp, M.

    2001-01-02

    The RIKEN-BNL Research Center workshop on ''Future Transversity Measurements'' was held at BNL from September 18-20, 2000. The main goal of the workshop was to explore future measurements of transversity distributions. This issue is of importance to the RHIC experiments, which will study polarized proton-proton collisions with great precision. One of the workshop's goals was to enhance interactions between the DIS community at HERA and the spin community at RHIC in this field. The workshop has been well received by the participants; the number of 69 registered participants demonstrates broad interest in the workshop's topics. The program contained 35 talks and there was ample time for lively discussions. The program covered all recent work in the field and in addition some very elucidating educational talks were given. At the workshop the present status of the field was discussed and it has succeeded in stimulating new experimental and theoretical studies (e.g. model calculations for interference fragmentation functions (IFF), IFF analysis at DELPHI). It also functioned to focus attention on the open questions that need to be resolved for near future experiments. In general, the conclusions were optimistic, i.e. measuring the transversity functions seems to be possible, although some new experimental hurdles will have to be taken.

  18. Phenotype-gene: 736 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 736 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u3ria224u912i abnormal for trait of behavior...eb. Science 307(5712):1111-3. http://metadb.riken.jp/db/SciNetS_ria224i/cria224u4ria224u15618487i abnormal for trait of behavior

  19. Status of beam line detectors for the BigRIPS fragment separator at RIKEN RI Beam Factory. Issues on high rates and resolution

    International Nuclear Information System (INIS)

    Sato, Yuki; Fukuda, Naoki; Takeda, Hiroyuki

    2015-01-01

    A multiple sampling ionization chamber (MUSIC) and parallel-plate avalanche counters (PPACs) were installed within the superconducting in-flight separator, named BigRIPS, at the RIKEN Nishina Center for particle identification of RI beams. The MUSIC detector showed negligible charge collection inefficiency from recombination of electrons and ions, up to a 99-kcps incidence rate for high-energy heavy ions. For the PPAC detectors, the electrical discharge durability for incident heavy ions was improved by changing the electrode material. Finally, we designed a single crystal diamond detector, which is under development for TOF measurements of high-energy heavy ions, that has a very fast response time (pulse width <1 ns). (author)

  20. Status of Beam Line Detectors for the BigRIPS Fragment Separator at RIKEN RI Beam Factory: Issues on High Rates and Resolution

    Science.gov (United States)

    Sato, Yuki; Fukuda, Naoki; Takeda, Hiroyuki; Kameda, Daisuke; Suzuki, Hiroshi; Shimizu, Yohei; Ahn, DeukSoon; Murai, Daichi; Inabe, Naohito; Shimaoka, Takehiro; Tsubota, Masakatsu; Kaneko, Junichi H.; Chayahara, Akiyoshi; Umezawa, Hitoshi; Shikata, Shinichi; Kumagai, Hidekazu; Murakami, Hiroyuki; Sato, Hiromi; Yoshida, Koichi; Kubo, Toshiyuki

    A multiple sampling ionization chamber (MUSIC) and parallel-plate avalanche counters (PPACs) were installed within the superconducting in-flight separator, named BigRIPS, at the RIKEN Nishina Center for particle identification of RI beams. The MUSIC detector showed negligible charge collection inefficiency from recombination of electrons and ions, up to a 99-kcps incidence rate for high-energy heavy ions. For the PPAC detectors, the electrical discharge durability for incident heavy ions was improved by changing the electrode material. Finally, we designed a single crystal diamond detector, which is under development for TOF measurements of high-energy heavy ions, that has a very fast response time (pulse width <1 ns).

  1. Focal plane detector for QDD spectrography in Institute of Nuclear Study and detector for SMART 2nd focal plane in RIKEN

    Energy Technology Data Exchange (ETDEWEB)

    Fuchi, Yoshihide [Tokyo Univ., Tanashi (Japan). Inst. for Nuclear Study

    1996-09-01

    The focal plane detector for QDD spectrography in Institute of Nuclear Study was composed of drift space and a proportional counter tube, and the latter is composed of position detector and two delta E detector for recognizing the particles. In this detector, a uniform parallel electric field can be obtained by placing a guard plate at the same height as that of a drift plate outer place of the detector. On the other hand, the detector for SMART 2nd focal plate in RIKEN is composed of drift space and a single wire proportional counter, and has two cathode read out single wire drift counters set so as to hold the focal plane. (G.K.)

  2. A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis.

    NARCIS (Netherlands)

    Emond-Rheault, Jean-Guillaume; Jeukens, Julie; Freschi, Luca; Kukavica-Ibrulj, Irena; Boyle, Brian; Dupont, Marie-Josée; Colavecchio, Anna; Barrere, Virginie; Cadieux, Brigitte; Arya, Gitanjali; Bekal, Sadjia; Berry, Chrystal; Burnett, Elton; Cavestri, Camille; Chapin, Travis K; Crouse, Alanna; Daigle, France; Danyluk, Michelle D; Delaquis, Pascal; Dewar, Ken; Doualla-Bell, Florence; Fliss, Ismail; Fong, Karen; Fournier, Eric; Franz, Eelco; Garduno, Rafael; Gill, Alexander; Gruenheid, Samantha; Harris, Linda; Huang, Carol B; Huang, Hongsheng; Johnson, Roger; Joly, Yann; Kerhoas, Maud; Kong, Nguyet; Lapointe, Gisèle; Larivière, Line; Loignon, Stéphanie; Malo, Danielle; Moineau, Sylvain; Mottawea, Walid; Mukhopadhyay, Kakali; Nadon, Céline; Nash, John; Ngueng Feze, Ida; Ogunremi, Dele; Perets, Ann; Pilar, Ana V; Reimer, Aleisha R; Robertson, James; Rohde, John; Sanderson, Kenneth E; Song, Lingqiao; Stephan, Roger; Tamber, Sandeep; Thomassin, Paul; Tremblay, Denise; Usongo, Valentine; Vincent, Caroline; Wang, Siyun; Weadge, Joel T; Wiedmann, Martin; Wijnands, Lucas; Wilson, Emily D; Wittum, Thomas; Yoshida, Catherine; Youfsi, Khadija; Zhu, Lei; Weimer, Bart C; Goodridge, Lawrence; Levesque, Roger C

    2017-01-01

    The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided

  3. Growing trend of CE at the omics level: the frontier of systems biology--an update.

    Science.gov (United States)

    Ban, Eunmi; Park, Soo Hyun; Kang, Min-Jung; Lee, Hyun-Jung; Song, Eun Joo; Yoo, Young Sook

    2012-01-01

    Omics is the study of proteins, peptides, genes, and metabolites in living organisms. Systems biology aims to understand the system through the study of the relationship between elements such as genes and proteins in biological system. Recently, systems biology emerged as the result of the advanced development of high-throughput analysis technologies such as DNA sequencers, DNA arrays, and mass spectrometry for omics studies. Among a number of analytical tools and technologies, CE and CE coupled to MS are promising and relatively rapidly developing tools with the potential to provide qualitative and quantitative analyses of biological molecules. With an emphasis on CE for systems biology, this review summarizes the method developments and applications of CE for the genomic, transcriptomic, proteomic, and metabolomic studies focusing on the drug discovery and disease diagnosis and therapies since 2009. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Proceedings of RIKEN BNL Research Center Workshop: Progress in High-pT Physics at RHIC

    Energy Technology Data Exchange (ETDEWEB)

    Bazilevsky, A.; Bland, L.; Vogelsang, W.

    2010-03-17

    This volume archives the presentations at the RIKEN BNL Research Center workshop 'Progress in High-PT Physics at RHIC', held at BNL in March 2010. Much has been learned from high-p{sub T} physics after 10 years of RHIC operations for heavy-ion collisions, polarized proton collisions and d+Au collisions. The workshop focused on recent progress in these areas by both theory and experiment. The first morning saw review talks on the theory of RHIC high-p{sub T} physics by G. Sterman and J. Soffer, and on the experimental results by M. Tannenbaum. One of the most exciting recent results from the RHIC spin program is the first observation of W bosons and their associated single-spin asymmetry. The new preliminary data were reported on the first day of our workshop, along with a theoretical perspective. There also were detailed discussions on the global analysis of polarized parton distributions, including the knowledge on gluon polarization and the impact of the W-data. The main topic of the second workshop day were single-transverse spin asymmetries and their analysis in terms of transverse-momentum dependent parton distributions. There is currently much interest in a future Drell-Yan program at RHIC, thanks to the exciting physics opportunities this would offer. This was addressed in some of the talks. There also were presentations on the latest results on transverse-spin physics from HERMES and BELLE. On the final day of the workshop, the focus shifted toward forward and small-x physics at RHIC, which has become a cornerstone of the whole RHIC program. Exciting new data were presented and discussed in terms of their possible implications for our understanding of strong color-field phenomena in QCD. In the afternoon, there were discussions of nuclear parton distributions and jet observables, among them fragmentation. The workshop was concluded with outlooks toward the near-term (LHC, JLab) and longer-term (EIC) future. The workshop has been a great success

  5. supraHex: An R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map☆

    Science.gov (United States)

    Fang, Hai; Gough, Julian

    2014-01-01

    Biologists are increasingly confronted with the challenge of quickly understanding genome-wide biological data, which usually involve a large number of genomic coordinates (e.g. genes) but a much smaller number of samples. To meet the need for data of this shape, we present an open-source package called ‘supraHex’ for training, analysing and visualising omics data. This package devises a supra-hexagonal map to self-organise the input data, offers scalable functionalities for post-analysing the map, and more importantly, allows for overlaying additional data for multilayer omics data comparisons. Via applying to DNA replication timing data of mouse embryogenesis, we demonstrate that supraHex is capable of simultaneously carrying out gene clustering and sample correlation, providing intuitive visualisation at each step of the analysis. By overlaying CpG and expression data onto the trained replication-timing map, we also show that supraHex is able to intuitively capture an inherent relationship between late replication, low CpG density promoters and low expression levels. As part of the Bioconductor project, supraHex makes accessible to a wide community in a simple way, what would otherwise be a complex framework for the ultrafast understanding of any tabular omics data, both scientifically and artistically. This package can run on Windows, Mac and Linux, and is freely available together with many tutorials on featuring real examples at http://supfam.org/supraHex. PMID:24309102

  6. Towards a Universal Approach Based on Omics Technologies for the Quality Control of Food.

    Science.gov (United States)

    Ferri, Emanuele; Galimberti, Andrea; Casiraghi, Maurizio; Airoldi, Cristina; Ciaramelli, Carlotta; Palmioli, Alessandro; Mezzasalma, Valerio; Bruni, Ilaria; Labra, Massimo

    2015-01-01

    In the last decades, food science has greatly developed, turning from the consideration of food as mere source of energy to a growing awareness on its importance for health and particularly in reducing the risk of diseases. Such vision led to an increasing attention towards the origin and quality of raw materials as well as their derived food products. The continuous advance in molecular biology allowed setting up efficient and universal omics tools to unequivocally identify the origin of food items and their traceability. In this review, we considered the application of a genomics approach known as DNA barcoding in characterizing the composition of foodstuffs and its traceability along the food supply chain. Moreover, metabolomics analytical strategies based on Nuclear Magnetic Resonance (NMR) and Mass Spectroscopy (MS) were discussed as they also work well in evaluating food quality. The combination of both approaches allows us to define a sort of molecular labelling of food that is easily understandable by the operators involved in the food sector: producers, distributors, and consumers. Current technologies based on digital information systems such as web platforms and smartphone apps can facilitate the adoption of such molecular labelling.

  7. Towards a Universal Approach Based on Omics Technologies for the Quality Control of Food

    Directory of Open Access Journals (Sweden)

    Emanuele Ferri

    2015-01-01

    Full Text Available In the last decades, food science has greatly developed, turning from the consideration of food as mere source of energy to a growing awareness on its importance for health and particularly in reducing the risk of diseases. Such vision led to an increasing attention towards the origin and quality of raw materials as well as their derived food products. The continuous advance in molecular biology allowed setting up efficient and universal omics tools to unequivocally identify the origin of food items and their traceability. In this review, we considered the application of a genomics approach known as DNA barcoding in characterizing the composition of foodstuffs and its traceability along the food supply chain. Moreover, metabolomics analytical strategies based on Nuclear Magnetic Resonance (NMR and Mass Spectroscopy (MS were discussed as they also work well in evaluating food quality. The combination of both approaches allows us to define a sort of molecular labelling of food that is easily understandable by the operators involved in the food sector: producers, distributors, and consumers. Current technologies based on digital information systems such as web platforms and smartphone apps can facilitate the adoption of such molecular labelling.

  8. Towards a Universal Approach Based on Omics Technologies for the Quality Control of Food

    Science.gov (United States)

    Ferri, Emanuele; Airoldi, Cristina; Ciaramelli, Carlotta; Palmioli, Alessandro; Bruni, Ilaria

    2015-01-01

    In the last decades, food science has greatly developed, turning from the consideration of food as mere source of energy to a growing awareness on its importance for health and particularly in reducing the risk of diseases. Such vision led to an increasing attention towards the origin and quality of raw materials as well as their derived food products. The continuous advance in molecular biology allowed setting up efficient and universal omics tools to unequivocally identify the origin of food items and their traceability. In this review, we considered the application of a genomics approach known as DNA barcoding in characterizing the composition of foodstuffs and its traceability along the food supply chain. Moreover, metabolomics analytical strategies based on Nuclear Magnetic Resonance (NMR) and Mass Spectroscopy (MS) were discussed as they also work well in evaluating food quality. The combination of both approaches allows us to define a sort of molecular labelling of food that is easily understandable by the operators involved in the food sector: producers, distributors, and consumers. Current technologies based on digital information systems such as web platforms and smartphone apps can facilitate the adoption of such molecular labelling. PMID:26783518

  9. How integration of global omics-data could help preparing for pandemics - a scent of influenza

    NARCIS (Netherlands)

    Bos, Lieuwe D. J.; de Jong, Menno D.; Sterk, Peter J.; Schultz, Marcus J.

    2014-01-01

    Pandemics caused by novel emerging or re-emerging infectious diseases could lead to high mortality and morbidity world-wide when left uncontrolled. In this perspective, we evaluate the possibility of integration of global omics-data in order to timely prepare for pandemics. Such an approach requires

  10. Open standards for cascade models for RHIC: Volume 1. Proceedings of RIKEN BNL Research Center workshop

    International Nuclear Information System (INIS)

    1997-01-01

    It is widely recognized that cascade models are potentially effective and powerful tools for interpreting and predicting multi-particle observables in heavy ion physics. However, the lack of common standards, documentation, version control, and accessibility have made it difficult to apply objective scientific criteria for evaluating the many physical and algorithmic assumptions or even to reproduce some published results. The first RIKEN Research Center workshop was proposed by Yang Pang to address this problem by establishing open standards for original codes for applications to nuclear collisions at RHIC energies. The aim of this first workshop is: (1) to prepare a WWW depository site for original source codes and detailed documentation with examples; (2) to develop and perform standardized test for the models such as Lorentz invariance, kinetic theory comparisons, and thermodynamic simulations; (3) to publish a compilation of results of the above work in a journal e.g., ''Heavy Ion Physics''; and (4) to establish a policy statement on a set of minimal requirements for inclusion in the OSCAR-WWW depository

  11. Growing trend of CE at the omics level: the frontier of systems biology.

    Science.gov (United States)

    Oh, Eulsik; Hasan, Md Nabiul; Jamshed, Muhammad; Park, Soo Hyun; Hong, Hye-Min; Song, Eun Joo; Yoo, Young Sook

    2010-01-01

    In a novel attempt to comprehend the complexity of life, systems biology has recently emerged as a state-of-the-art approach for biological research in contrast to the reductionist approaches that have been used in molecular cell biology since the 1950s. Because a massive amount of information is required in many systems biology studies of life processes, we have increasingly come to depend on techniques that provide high-throughput omics data. CE and CE coupled to MS have served as powerful analytical tools for providing qualitative and quantitative omics data. Recent systems biology studies have focused strongly on the diagnosis and treatment of diseases. The increasing number of clinical research papers on drug discovery and disease therapies reflects this growing interest among scientists. Since such clinical research reflects one of the ultimate purposes of bioscience, these trends will be sustained for a long time. Thus, this review mainly focuses on the application of CE and CE-MS in diagnosis as well as on the latest CE methods developed. Furthermore, we outline the new challenges that arose in 2008 and later in elucidating the system-level functions of the bioconstituents of living organisms.

  12. Robust Selection Algorithm (RSA) for Multi-Omic Biomarker Discovery; Integration with Functional Network Analysis to Identify miRNA Regulated Pathways in Multiple Cancers.

    Science.gov (United States)

    Sehgal, Vasudha; Seviour, Elena G; Moss, Tyler J; Mills, Gordon B; Azencott, Robert; Ram, Prahlad T

    2015-01-01

    MicroRNAs (miRNAs) play a crucial role in the maintenance of cellular homeostasis by regulating the expression of their target genes. As such, the dysregulation of miRNA expression has been frequently linked to cancer. With rapidly accumulating molecular data linked to patient outcome, the need for identification of robust multi-omic molecular markers is critical in order to provide clinical impact. While previous bioinformatic tools have been developed to identify potential biomarkers in cancer, these methods do not allow for rapid classification of oncogenes versus tumor suppressors taking into account robust differential expression, cutoffs, p-values and non-normality of the data. Here, we propose a methodology, Robust Selection Algorithm (RSA) that addresses these important problems in big data omics analysis. The robustness of the survival analysis is ensured by identification of optimal cutoff values of omics expression, strengthened by p-value computed through intensive random resampling taking into account any non-normality in the data and integration into multi-omic functional networks. Here we have analyzed pan-cancer miRNA patient data to identify functional pathways involved in cancer progression that are associated with selected miRNA identified by RSA. Our approach demonstrates the way in which existing survival analysis techniques can be integrated with a functional network analysis framework to efficiently identify promising biomarkers and novel therapeutic candidates across diseases.

  13. Longitudinal Omics Modelling and Integration in Clinical Metabonomics Research: challenges in childhood metabolic health research

    Directory of Open Access Journals (Sweden)

    Peter eSperisen

    2015-08-01

    Full Text Available Systems biology is an important approach for deciphering the complex processes in health maintenance and the etiology of metabolic diseases. Such integrative methodologies will help better understand the molecular mechanisms involved in growth and development throughout childhood, and consequently will result in new insights about metabolic and nutritional requirements of infants, children and adults. To achieve this, a better understanding of the physiological processes at anthropometric, cellular and molecular level for any given individual is needed. In this respect, novel omics technologies in combination with sophisticated data modelling techniques are key. Due to the highly complex network of influential factors determining individual trajectories, it becomes imperative to develop proper tools and solutions that will comprehensively model biological information related to growth and maturation of our body functions. The aim of this review and perspective is to evaluate, succinctly, promising data analysis approaches to enable data integration for clinical research, with an emphasis on the longitudinal component. Approaches based on empirical and mechanistic modelling of omics data are essential to leverage findings from high dimensional omics datasets and enable biological interpretation and clinical translation. On the one hand, empirical methods, which provide quantitative descriptions of patterns in the data, are mostly used for exploring and mining datasets. On the other hand, mechanistic models are based on an understanding of the behavior of a system’s components and condense information about the known functions, allowing robust and reliable analyses to be performed by bioinformatics pipelines and similar tools. Herein, we will illustrate current examples, challenges and perspectives in the applications of empirical and mechanistic modelling in the context of childhood metabolic health research.

  14. GENEASE: Real time bioinformatics tool for multi-omics and disease ontology exploration, analysis and visualization.

    Science.gov (United States)

    Ghandikota, Sudhir; Hershey, Gurjit K Khurana; Mersha, Tesfaye B

    2018-03-24

    Advances in high-throughput sequencing technologies have made it possible to generate multiple omics data at an unprecedented rate and scale. The accumulation of these omics data far outpaces the rate at which biologists can mine and generate new hypothesis to test experimentally. There is an urgent need to develop a myriad of powerful tools to efficiently and effectively search and filter these resources to address specific post-GWAS functional genomics questions. However, to date, these resources are scattered across several databases and often lack a unified portal for data annotation and analytics. In addition, existing tools to analyze and visualize these databases are highly fragmented, resulting researchers to access multiple applications and manual interventions for each gene or variant in an ad hoc fashion until all the questions are answered. In this study, we present GENEASE, a web-based one-stop bioinformatics tool designed to not only query and explore multi-omics and phenotype databases (e.g., GTEx, ClinVar, dbGaP, GWAS Catalog, ENCODE, Roadmap Epigenomics, KEGG, Reactome, Gene and Phenotype Ontology) in a single web interface but also to perform seamless post genome-wide association downstream functional and overlap analysis for non-coding regulatory variants. GENEASE accesses over 50 different databases in public domain including model organism-specific databases to facilitate gene/variant and disease exploration, enrichment and overlap analysis in real time. It is a user-friendly tool with point-and-click interface containing links for support information including user manual and examples. GENEASE can be accessed freely at http://research.cchmc.org/mershalab/genease_new/login.html. Tesfaye.Mersha@cchmc.org, Sudhir.Ghandikota@cchmc.org. Supplementary data are available at Bioinformatics online.

  15. MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling

    Energy Technology Data Exchange (ETDEWEB)

    Burnum-Johnson, Kristin E.; Kyle, Jennifer E.; Eisfeld, Amie J.; Casey, Cameron P.; Stratton, Kelly G.; Gonzalez, Juan F.; Habyarimana, Fabien; Negretti, Nicholas M.; Sims, Amy C.; Chauhan, Sadhana; Thackray, Larissa B.; Halfmann, Peter J.; Walters, Kevin B.; Kim, Young-Mo; Zink, Erika M.; Nicora, Carrie D.; Weitz, Karl K.; Webb-Robertson, Bobbie-Jo M.; Nakayasu, Ernesto S.; Ahmer, Brian; Konkel, Michael E.; Motin, Vladimir; Baric, Ralph S.; Diamond, Michael S.; Kawaoka, Yoshihiro; Waters, Katrina M.; Smith, Richard D.; Metz, Thomas O.

    2017-01-01

    The continued emergence and spread of infectious agents is of increasing concern due to increased population growth and the associated increased livestock production to meet food demands, increased urbanization and land-use changes, and greater travel. A systems biology approach to infectious disease research can significantly advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can only take place subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements. This metabolite, protein and lipid extraction (MPLEx) method resulted in complete inactivation of bacterial and viral pathogens with exposed lipid membranes, including Yersinia pestis, Salmonella Typhimurium, and Campylobacter jejuni in pure culture, and Yersinia pestis, Campylobacter jejuni, West Nile, MERS-CoV, Ebola, and influenza H7N9 viruses in infection studies. Partial inactivation was observed for pathogens without exposed lipid membranes including 99.99% inactivation of community-associated methicillin-resistant Staphylococcus aureus, 99.6% and >99% inactivation of Clostridium difficile spores and vegetative cells, respectively, and 50% inactivation of adenovirus type 5. To demonstrate that MPLEx yields biomaterial of sufficient quality for subsequent multi-omics analyses, we highlight select proteomics, metabolomics and lipidomics data from human epithelial lung cells infected with wild-type and mutant forms of influenza H7N9. We believe that MPLEx will facilitate systems biology studies of infectious samples by enabling simultaneous pathogen inactivation and multi-omics

  16. 'Omics analysis of low dose acetaminophen intake demonstrates novel response pathways in humans

    International Nuclear Information System (INIS)

    Jetten, Marlon J.A.; Gaj, Stan; Ruiz-Aracama, Ainhoa; Kok, Theo M. de; Delft, Joost H.M. van; Lommen, Arjen; Someren, Eugene P. van; Jennen, Danyel G.J.; Claessen, Sandra M.; Peijnenburg, Ad A.C.M.; Stierum, Rob H.; Kleinjans, Jos C.S.

    2012-01-01

    Acetaminophen is the primary cause of acute liver toxicity in Europe/USA, which led the FDA to reconsider recommendations concerning safe acetaminophen dosage/use. Unfortunately, the current tests for liver toxicity are no ideal predictive markers for liver injury, i.e. they only measure acetaminophen exposure after profound liver toxicity has already occurred. Furthermore, these tests do not provide mechanistic information. Here, 'omics techniques (global analysis of metabolomic/gene-expression responses) may provide additional insight. To better understand acetaminophen-induced responses at low doses, we evaluated the effects of (sub-)therapeutic acetaminophen doses on metabolite formation and global gene-expression changes (including, for the first time, full-genome human miRNA expression changes) in blood/urine samples from healthy human volunteers. Many known and several new acetaminophen-metabolites were detected, in particular in relation to hepatotoxicity-linked, oxidative metabolism of acetaminophen. Transcriptomic changes indicated immune-modulating effects (2 g dose) and oxidative stress responses (4 g dose). For the first time, effects of acetaminophen on full-genome human miRNA expression have been considered and confirmed the findings on mRNA level. 'Omics techniques outperformed clinical chemistry tests and revealed novel response pathways to acetaminophen in humans. Although no definitive conclusion about potential immunotoxic effects of acetaminophen can be drawn from this study, there are clear indications that the immune system is triggered even after intake of low doses of acetaminophen. Also, oxidative stress-related gene responses, similar to those seen after high dose acetaminophen exposure, suggest the occurrence of possible pre-toxic effects of therapeutic acetaminophen doses. Possibly, these effects are related to dose-dependent increases in levels of hepatotoxicity-related metabolites. -- Highlights: ► 'Omics techniques outperformed

  17. Advances in Integrating Traditional and Omic Biomarkers When Analyzing the Effects of the Mediterranean Diet Intervention in Cardiovascular Prevention

    Science.gov (United States)

    Fitó, Montserrat; Melander, Olle; Martínez, José Alfredo; Toledo, Estefanía; Carpéné, Christian; Corella, Dolores

    2016-01-01

    Intervention with Mediterranean diet (MedDiet) has provided a high level of evidence in primary prevention of cardiovascular events. Besides enhancing protection from classical risk factors, an improvement has also been described in a number of non-classical ones. Benefits have been reported on biomarkers of oxidation, inflammation, cellular adhesion, adipokine production, and pro-thrombotic state. Although the benefits of the MedDiet have been attributed to its richness in antioxidants, the mechanisms by which it exercises its beneficial effects are not well known. It is thought that the integration of omics including genomics, transcriptomics, epigenomics, and metabolomics, into studies analyzing nutrition and cardiovascular diseases will provide new clues regarding these mechanisms. However, omics integration is still in its infancy. Currently, some single-omics analyses have provided valuable data, mostly in the field of genomics. Thus, several gene-diet interactions in determining both intermediate (plasma lipids, etc.) and final cardiovascular phenotypes (stroke, myocardial infarction, etc.) have been reported. However, few studies have analyzed changes in gene expression and, moreover very few have focused on epigenomic or metabolomic biomarkers related to the MedDiet. Nevertheless, these preliminary results can help to better understand the inter-individual differences in cardiovascular risk and dietary response for further applications in personalized nutrition. PMID:27598147

  18. Using combined bio-omics methods to evaluate the complicated toxic effects of mixed chemical wastewater and its treated effluent

    International Nuclear Information System (INIS)

    Zhang, Yan; Deng, Yongfeng; Zhao, Yanping; Ren, Hongqiang

    2014-01-01

    Highlights: • Mice exposed to mixed chemical wastewater and its treated effluent for 90 days. • Hepatic transcriptomic alterations were analyzed by digital gene expression. • Serum metabolomic alterations were analyzed by proton nuclear magnetic resonance. • The water samples induced disruption of lipid metabolism and hepatotoxicity. • Omics approaches are valuable to evaluate the complicated toxicity of wastewater. - Abstract: Mixed chemical wastewaters (MCWW) from industrial park contain complex mixtures of trace contaminants, which cannot be effectively removed by wastewater treatment plants (WWTP) and have become an unignored threat to ambient environment. However, limited information is available to evaluate the complicated toxic effects of MCWW and its effluent from wastewater treatment plant (WTPE) from the perspective of bio-omics. In this study, mice were exposed to the MCWW and WTPE for 90 days and distinct differences in the hepatic transcriptome and serum metabolome were analyzed by digital gene expression (DGE) and proton nuclear magnetic resonance ( 1 H-NMR) spectra, respectively. Our results indicated that disruption of lipid metabolism in liver and hepatotoxicity were induced by both MCWW and WTPE exposure. WTPE is still a health risk to the environment, which is in need of more attention. Furthermore, we demonstrated the potential ability of bio-omics approaches for evaluating toxic effects of MCWW and WTPE

  19. Using combined bio-omics methods to evaluate the complicated toxic effects of mixed chemical wastewater and its treated effluent

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yan; Deng, Yongfeng; Zhao, Yanping; Ren, Hongqiang, E-mail: hqren@nju.edu.cn

    2014-05-01

    Highlights: • Mice exposed to mixed chemical wastewater and its treated effluent for 90 days. • Hepatic transcriptomic alterations were analyzed by digital gene expression. • Serum metabolomic alterations were analyzed by proton nuclear magnetic resonance. • The water samples induced disruption of lipid metabolism and hepatotoxicity. • Omics approaches are valuable to evaluate the complicated toxicity of wastewater. - Abstract: Mixed chemical wastewaters (MCWW) from industrial park contain complex mixtures of trace contaminants, which cannot be effectively removed by wastewater treatment plants (WWTP) and have become an unignored threat to ambient environment. However, limited information is available to evaluate the complicated toxic effects of MCWW and its effluent from wastewater treatment plant (WTPE) from the perspective of bio-omics. In this study, mice were exposed to the MCWW and WTPE for 90 days and distinct differences in the hepatic transcriptome and serum metabolome were analyzed by digital gene expression (DGE) and proton nuclear magnetic resonance ({sup 1}H-NMR) spectra, respectively. Our results indicated that disruption of lipid metabolism in liver and hepatotoxicity were induced by both MCWW and WTPE exposure. WTPE is still a health risk to the environment, which is in need of more attention. Furthermore, we demonstrated the potential ability of bio-omics approaches for evaluating toxic effects of MCWW and WTPE.

  20. A Community Multi-Omics Approach towards the Assessment of Surface Water Quality in an Urban River System

    Directory of Open Access Journals (Sweden)

    David J. Beale

    2017-03-01

    Full Text Available A multi-omics approach was applied to an urban river system (the Brisbane River (BR, Queensland, Australia in order to investigate surface water quality and characterize the bacterial population with respect to water contaminants. To do this, bacterial metagenomic amplicon-sequencing using Illumina next-generation sequencing (NGS of the V5–V6 hypervariable regions of the 16S rRNA gene and untargeted community metabolomics using gas chromatography coupled with mass spectrometry (GC-MS were utilized. The multi-omics data, in combination with fecal indicator bacteria (FIB counts, trace metal concentrations (by inductively coupled plasma mass spectrometry (ICP-MS and in-situ water quality measurements collected from various locations along the BR were then used to assess the health of the river ecosystem. Sites sampled represented the transition from less affected (upstream to polluted (downstream environments along the BR. Chemometric analysis of the combined datasets indicated a clear separation between the sampled environments. Burkholderiales and Cyanobacteria were common key factors for differentiation of pristine waters. Increased sugar alcohol and short-chain fatty acid production was observed by Actinomycetales and Rhodospirillaceae that are known to form biofilms in urban polluted and brackish waters. Results from this study indicate that a multi-omics approach enables a deep understanding of the health of an aquatic ecosystem, providing insight into the bacterial diversity present and the metabolic output of the population when exposed to environmental contaminants.

  1. Omic personality: implications of stable transcript and methylation profiles for personalized medicine.

    Science.gov (United States)

    Tabassum, Rubina; Sivadas, Ambily; Agrawal, Vartika; Tian, Haozheng; Arafat, Dalia; Gibson, Greg

    2015-08-13

    Personalized medicine is predicated on the notion that individual biochemical and genomic profiles are relatively constant in times of good health and to some extent predictive of disease or therapeutic response. We report a pilot study quantifying gene expression and methylation profile consistency over time, addressing the reasons for individual uniqueness, and its relation to N = 1 phenotypes. Whole blood samples from four African American women, four Caucasian women, and four Caucasian men drawn from the Atlanta Center for Health Discovery and Well Being study at three successive 6-month intervals were profiled by RNA-Seq, miRNA-Seq, and Illumina Methylation 450 K arrays. Standard regression approaches were used to evaluate the proportion of variance for each type of omic measure among individuals, and to quantify correlations among measures and with clinical attributes related to wellness. Longitudinal omic profiles were in general highly consistent over time, with an average of 67 % variance in transcript abundance, 42 % in CpG methylation level (but 88 % for the most differentiated CpG per gene), and 50 % in miRNA abundance among individuals, which are all comparable to 74 % variance among individuals for 74 clinical traits. One third of the variance could be attributed to differential blood cell type abundance, which was also fairly stable over time, and a lesser amount to expression quantitative trait loci (eQTL) effects. Seven conserved axes of covariance that capture diverse aspects of immune function explained over half of the variance. These axes also explained a considerable proportion of individually extreme transcript abundance, namely approximately 100 genes that were significantly up-regulated or down-regulated in each person and were in some cases enriched for relevant gene activities that plausibly associate with clinical attributes. A similar fraction of genes had individually divergent methylation levels, but these did not overlap with the

  2. GeneLab: Open Science For Exploration

    Science.gov (United States)

    Galazka, Jonathan

    2018-01-01

    The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. The GeneLab project houses spaceflight and spaceflight-relevant multi-omics data in a publicly accessible data commons, and collaborates with NASA-funded principal investigators to maximize the omics data from spaceflight and spaceflight-relevant experiments. I will discuss the current status of GeneLab and give specific examples of how the GeneLab data system has been used to gain insight into how biology responds to spaceflight conditions.

  3. Genelab: Scientific Partnerships and an Open-Access Database to Maximize Usage of Omics Data from Space Biology Experiments

    Science.gov (United States)

    Reinsch, S. S.; Galazka, J..; Berrios, D. C; Chakravarty, K.; Fogle, H.; Lai, S.; Bokyo, V.; Timucin, L. R.; Tran, P.; Skidmore, M.

    2016-01-01

    NASA's mission includes expanding our understanding of biological systems to improve life on Earth and to enable long-duration human exploration of space. The GeneLab Data System (GLDS) is NASA's premier open-access omics data platform for biological experiments. GLDS houses standards-compliant, high-throughput sequencing and other omics data from spaceflight-relevant experiments. The GeneLab project at NASA-Ames Research Center is developing the database, and also partnering with spaceflight projects through sharing or augmentation of experiment samples to expand omics analyses on precious spaceflight samples. The partnerships ensure that the maximum amount of data is garnered from spaceflight experiments and made publically available as rapidly as possible via the GLDS. GLDS Version 1.0, went online in April 2015. Software updates and new data releases occur at least quarterly. As of October 2016, the GLDS contains 80 datasets and has search and download capabilities. Version 2.0 is slated for release in September of 2017 and will have expanded, integrated search capabilities leveraging other public omics databases (NCBI GEO, PRIDE, MG-RAST). Future versions in this multi-phase project will provide a collaborative platform for omics data analysis. Data from experiments that explore the biological effects of the spaceflight environment on a wide variety of model organisms are housed in the GLDS including data from rodents, invertebrates, plants and microbes. Human datasets are currently limited to those with anonymized data (e.g., from cultured cell lines). GeneLab ensures prompt release and open access to high-throughput genomics, transcriptomics, proteomics, and metabolomics data from spaceflight and ground-based simulations of microgravity, radiation or other space environment factors. The data are meticulously curated to assure that accurate experimental and sample processing metadata are included with each data set. GLDS download volumes indicate strong

  4. Mapping epistasis and environment × QTX interaction based on four -omics genotypes for the detected QTX loci controlling complex traits in tobacco

    Directory of Open Access Journals (Sweden)

    Liyuan Zhou

    2013-12-01

    Full Text Available Using newly developed methods and software, association mapping was conducted for chromium content and total sugar in tobacco leaf, based on four -omics datasets. Our objective was to collect data on genotype and phenotype for 60 leaf samples at four developmental stages, from three plant architectural positions and for three cultivars that were grown in two locations. Association mapping was conducted to detect genetic variants at quantitative trait SNP (QTS loci, quantitative trait transcript (QTT differences, quantitative trait protein (QTP variability, and quantitative trait metabolite (QTM changes, which can be summarized as QTX locus variation. The total heritabilities of the four -omics loci for both traits tested were 23.60% for epistasis and 15.26% for treatment interaction. Epistasis and environment × treatment interaction had important impacts on complex traits at all -omics levels. For decreasing chromium content and increasing total sugar in tobacco leaf, six methylated loci can be directly used for marker-assisted selection, and expression of ten QTTs, seven QTPs and six QTMs can be modified by selection or cultivation.

  5. Time to "go large" on biofilm research: advantages of an omics approach.

    Science.gov (United States)

    Azevedo, Nuno F; Lopes, Susana P; Keevil, Charles W; Pereira, Maria O; Vieira, Maria J

    2009-04-01

    In nature, the biofilm mode of life is of great importance in the cell cycle for many microorganisms. Perhaps because of biofilm complexity and variability, the characterization of a given microbial system, in terms of biofilm formation potential, structure and associated physiological activity, in a large-scale, standardized and systematic manner has been hindered by the absence of high-throughput methods. This outlook is now starting to change as new methods involving the utilization of microtiter-plates and automated spectrophotometry and microscopy systems are being developed to perform large-scale testing of microbial biofilms. Here, we evaluate if the time is ripe to start an integrated omics approach, i.e., the generation and interrogation of large datasets, to biofilms--"biofomics". This omics approach would bring much needed insight into how biofilm formation ability is affected by a number of environmental, physiological and mutational factors and how these factors interplay between themselves in a standardized manner. This could then lead to the creation of a database where biofilm signatures are identified and interrogated. Nevertheless, and before embarking on such an enterprise, the selection of a versatile, robust, high-throughput biofilm growing device and of appropriate methods for biofilm analysis will have to be performed. Whether such device and analytical methods are already available, particularly for complex heterotrophic biofilms is, however, very debatable.

  6. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

    Science.gov (United States)

    Slenter, Denise N; Kutmon, Martina; Hanspers, Kristina; Riutta, Anders; Windsor, Jacob; Nunes, Nuno; Mélius, Jonathan; Cirillo, Elisa; Coort, Susan L; Digles, Daniela; Ehrhart, Friederike; Giesbertz, Pieter; Kalafati, Marianthi; Martens, Marvin; Miller, Ryan; Nishida, Kozo; Rieswijk, Linda; Waagmeester, Andra; Eijssen, Lars M T; Evelo, Chris T; Pico, Alexander R; Willighagen, Egon L

    2018-01-04

    WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. Recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. Here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in WikiPathways. Furthermore, we introduce an OpenAPI documentation of our web services and the FAIR (Findable, Accessible, Interoperable and Reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Effect of minimum strength of mirror magnetic field (Bmin) on production of highly charged heavy ions from RIKEN liquid-He-free super conducting electron-cyclotron resonance ion source (RAMSES)

    International Nuclear Information System (INIS)

    Arai, Hideyuki; Imanaka, Masashi; Lee, S.-M.Sang-Moo; Higurashi, Yoshihide; Nakagawa, Takahide; Kidera, Masanori; Kageyama, Tadashi; Kase, Masayuki; Yano, Yasushige; Aihara, Toshimitsu

    2002-01-01

    We measured the beam intensity of highly charged heavy ions (O, Ar and Kr ions) as a function of the minimum strength of mirror magnetic field (B min ) of the RIKEN liquid-He-free super conducting electron-cyclotron resonance ion source. In this experiment, we found that the optimum value of B min exists to maximize the beam intensity of highly charged heavy ions and the value was almost the same (∼0.49 T) for various charge state heavy ions

  8. A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection

    Energy Technology Data Exchange (ETDEWEB)

    Kaiser, Brooke LD; Li, Jie; Sanford, James A.; Kim, Young-Mo; Kronewitter, Scott R.; Jones, Marcus B.; Peterson, Christine; Peterson, Scott N.; Frank, Bryan C.; Purvine, Samuel O.; Brown, Joseph N.; Metz, Thomas O.; Smith, Richard D.; Heffron, Fred; Adkins, Joshua N.

    2013-06-26

    The potential for commensal microorganisms indigenous to a host (the ‘microbiome’ or ‘microbiota’) to alter infection outcome by influencing host-pathogen interplay is largely unknown. We used a multi-omics “systems” approach, incorporating proteomics, metabolomics, glycomics, and metagenomics, to explore the molecular interplay between the murine host, the pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium), and commensal gut microorganisms during intestinal infection with S. Typhimurium. We find proteomic evidence that S. Typhimurium thrives within the infected 129/SvJ mouse gut without antibiotic pre-treatment, inducing inflammation and disrupting the intestinal microbiome (e.g., suppressing Bacteroidetes and Firmicutes while promoting growth of Salmonella and Enterococcus). Alteration of the host microbiome population structure was highly correlated with gut environmental changes, including the accumulation of metabolites normally consumed by commensal microbiota. Finally, the less characterized phase of S. Typhimurium’s lifecycle was investigated, and both proteomic and glycomic evidence suggests S. Typhimurium may take advantage of increased fucose moieties to metabolize fucose while growing in the gut. The application of multiple omics measurements to Salmonella-induced intestinal inflammation provides insights into complex molecular strategies employed during pathogenesis between host, pathogen, and the microbiome.

  9. 'Omics analysis of low dose acetaminophen intake demonstrates novel response pathways in humans

    Energy Technology Data Exchange (ETDEWEB)

    Jetten, Marlon J.A.; Gaj, Stan [Department of Toxicogenomics, Maastricht University, Universitiessingel 50 6229 ER Maastricht (Netherlands); Ruiz-Aracama, Ainhoa [RIKILT, Institute of Food Safety, Wageningen UR, PO Box 230, 6700 AE, Wageningen (Netherlands); Kok, Theo M. de [Department of Toxicogenomics, Maastricht University, Universitiessingel 50 6229 ER Maastricht (Netherlands); Delft, Joost H.M. van, E-mail: j.vandelft@maastrichtuniversity.nl [Department of Toxicogenomics, Maastricht University, Universitiessingel 50 6229 ER Maastricht (Netherlands); Lommen, Arjen [RIKILT, Institute of Food Safety, Wageningen UR, PO Box 230, 6700 AE, Wageningen (Netherlands); Someren, Eugene P. van [Research Group Microbiology and Systems Biology, TNO, PO Box 360 3700 AJ Zeist (Netherlands); Jennen, Danyel G.J.; Claessen, Sandra M. [Department of Toxicogenomics, Maastricht University, Universitiessingel 50 6229 ER Maastricht (Netherlands); Peijnenburg, Ad A.C.M. [RIKILT, Institute of Food Safety, Wageningen UR, PO Box 230, 6700 AE, Wageningen (Netherlands); Stierum, Rob H. [Research Group Microbiology and Systems Biology, TNO, PO Box 360 3700 AJ Zeist (Netherlands); Kleinjans, Jos C.S. [Department of Toxicogenomics, Maastricht University, Universitiessingel 50 6229 ER Maastricht (Netherlands)

    2012-03-15

    Acetaminophen is the primary cause of acute liver toxicity in Europe/USA, which led the FDA to reconsider recommendations concerning safe acetaminophen dosage/use. Unfortunately, the current tests for liver toxicity are no ideal predictive markers for liver injury, i.e. they only measure acetaminophen exposure after profound liver toxicity has already occurred. Furthermore, these tests do not provide mechanistic information. Here, 'omics techniques (global analysis of metabolomic/gene-expression responses) may provide additional insight. To better understand acetaminophen-induced responses at low doses, we evaluated the effects of (sub-)therapeutic acetaminophen doses on metabolite formation and global gene-expression changes (including, for the first time, full-genome human miRNA expression changes) in blood/urine samples from healthy human volunteers. Many known and several new acetaminophen-metabolites were detected, in particular in relation to hepatotoxicity-linked, oxidative metabolism of acetaminophen. Transcriptomic changes indicated immune-modulating effects (2 g dose) and oxidative stress responses (4 g dose). For the first time, effects of acetaminophen on full-genome human miRNA expression have been considered and confirmed the findings on mRNA level. 'Omics techniques outperformed clinical chemistry tests and revealed novel response pathways to acetaminophen in humans. Although no definitive conclusion about potential immunotoxic effects of acetaminophen can be drawn from this study, there are clear indications that the immune system is triggered even after intake of low doses of acetaminophen. Also, oxidative stress-related gene responses, similar to those seen after high dose acetaminophen exposure, suggest the occurrence of possible pre-toxic effects of therapeutic acetaminophen doses. Possibly, these effects are related to dose-dependent increases in levels of hepatotoxicity-related metabolites. -- Highlights: ► 'Omics techniques

  10. Identification of "pathologs" (disease-related genes from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system

    Directory of Open Access Journals (Sweden)

    Socha Luis A

    2004-04-01

    Full Text Available Abstract Background A major goal in the post-genomic era is to identify and characterise disease susceptibility genes and to apply this knowledge to disease prevention and treatment. Rodents and humans have remarkably similar genomes and share closely related biochemical, physiological and pathological pathways. In this work we utilised the latest information on the mouse transcriptome as revealed by the RIKEN FANTOM2 project to identify novel human disease-related candidate genes. We define a new term "patholog" to mean a homolog of a human disease-related gene encoding a product (transcript, anti-sense or protein potentially relevant to disease. Rather than just focus on Mendelian inheritance, we applied the analysis to all potential pathologs regardless of their inheritance pattern. Results Bioinformatic analysis and human curation of 60,770 RIKEN full-length mouse cDNA clones produced 2,578 sequences that showed similarity (70–85% identity to known human-disease genes. Using a newly developed biological information extraction and annotation tool (FACTS in parallel with human expert analysis of 17,051 MEDLINE scientific abstracts we identified 182 novel potential pathologs. Of these, 36 were identified by computational tools only, 49 by human expert analysis only and 97 by both methods. These pathologs were related to neoplastic (53%, hereditary (24%, immunological (5%, cardio-vascular (4%, or other (14%, disorders. Conclusions Large scale genome projects continue to produce a vast amount of data with potential application to the study of human disease. For this potential to be realised we need intelligent strategies for data categorisation and the ability to link sequence data with relevant literature. This paper demonstrates the power of combining human expert annotation with FACTS, a newly developed bioinformatics tool, to identify novel pathologs from within large-scale mouse transcript datasets.

  11. From meta-omics to causality: experimental models for human microbiome research.

    Science.gov (United States)

    Fritz, Joëlle V; Desai, Mahesh S; Shah, Pranjul; Schneider, Jochen G; Wilmes, Paul

    2013-05-03

    Large-scale 'meta-omic' projects are greatly advancing our knowledge of the human microbiome and its specific role in governing health and disease states. A myriad of ongoing studies aim at identifying links between microbial community disequilibria (dysbiosis) and human diseases. However, due to the inherent complexity and heterogeneity of the human microbiome, cross-sectional, case-control and longitudinal studies may not have enough statistical power to allow causation to be deduced from patterns of association between variables in high-resolution omic datasets. Therefore, to move beyond reliance on the empirical method, experiments are critical. For these, robust experimental models are required that allow the systematic manipulation of variables to test the multitude of hypotheses, which arise from high-throughput molecular studies. Particularly promising in this respect are microfluidics-based in vitro co-culture systems, which allow high-throughput first-pass experiments aimed at proving cause-and-effect relationships prior to testing of hypotheses in animal models. This review focuses on widely used in vivo, in vitro, ex vivo and in silico approaches to study host-microbial community interactions. Such systems, either used in isolation or in a combinatory experimental approach, will allow systematic investigations of the impact of microbes on the health and disease of the human host. All the currently available models present pros and cons, which are described and discussed. Moreover, suggestions are made on how to develop future experimental models that not only allow the study of host-microbiota interactions but are also amenable to high-throughput experimentation.

  12. Omics/systems biology and cancer cachexia.

    Science.gov (United States)

    Gallagher, Iain J; Jacobi, Carsten; Tardif, Nicolas; Rooyackers, Olav; Fearon, Kenneth

    2016-06-01

    Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteristic of complex systems with the result that the end result is more than the sum of its parts. Recognition of the importance of emergent properties in biology led to the concept of systems biology wherein a holistic approach is taken to the biology at hand. Systems biology approaches will therefore play an important role in work to uncover key mechanisms with therapeutic potential in cancer cachexia. The 'omics' technologies provide a global view of biological systems. Genomics, transcriptomics, proteomics, lipidomics and metabolomics approaches all have application in the study of cancer cachexia to generate systems level models of the behaviour of this syndrome. The current work reviews recent applications of these technologies to muscle atrophy in general and cancer cachexia in particular with a view to progress towards integration of these approaches to better understand the pathology and potential treatment pathways in cancer cachexia. Copyright © 2016. Published by Elsevier Ltd.

  13. Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach.

    Science.gov (United States)

    Ali, Mehreen; Khan, Suleiman A; Wennerberg, Krister; Aittokallio, Tero

    2018-04-15

    Proteomics profiling is increasingly being used for molecular stratification of cancer patients and cell-line panels. However, systematic assessment of the predictive power of large-scale proteomic technologies across various drug classes and cancer types is currently lacking. To that end, we carried out the first pan-cancer, multi-omics comparative analysis of the relative performance of two proteomic technologies, targeted reverse phase protein array (RPPA) and global mass spectrometry (MS), in terms of their accuracy for predicting the sensitivity of cancer cells to both cytotoxic chemotherapeutics and molecularly targeted anticancer compounds. Our results in two cell-line panels demonstrate how MS profiling improves drug response predictions beyond that of the RPPA or the other omics profiles when used alone. However, frequent missing MS data values complicate its use in predictive modeling and required additional filtering, such as focusing on completely measured or known oncoproteins, to obtain maximal predictive performance. Rather strikingly, the two proteomics profiles provided complementary predictive signal both for the cytotoxic and targeted compounds. Further, information about the cellular-abundance of primary target proteins was found critical for predicting the response of targeted compounds, although the non-target features also contributed significantly to the predictive power. The clinical relevance of the selected protein markers was confirmed in cancer patient data. These results provide novel insights into the relative performance and optimal use of the widely applied proteomic technologies, MS and RPPA, which should prove useful in translational applications, such as defining the best combination of omics technologies and marker panels for understanding and predicting drug sensitivities in cancer patients. Processed datasets, R as well as Matlab implementations of the methods are available at https://github.com/mehr-een/bemkl-rbps. mehreen

  14. Emerging areas of science: Recommendations for Nursing Science Education from the Council for the Advancement of Nursing Science Idea Festival.

    Science.gov (United States)

    Henly, Susan J; McCarthy, Donna O; Wyman, Jean F; Heitkemper, Margaret M; Redeker, Nancy S; Titler, Marita G; McCarthy, Ann Marie; Stone, Patricia W; Moore, Shirley M; Alt-White, Anna C; Conley, Yvette P; Dunbar-Jacob, Jacqueline

    2015-01-01

    The Council for the Advancement of Nursing Science aims to "facilitate and recognize life-long nursing science career development" as an important part of its mission. In light of fast-paced advances in science and technology that are inspiring new questions and methods of investigation in the health sciences, the Council for the Advancement of Nursing Science convened the Idea Festival for Nursing Science Education and appointed the Idea Festival Advisory Committee (IFAC) to stimulate dialogue about linking PhD education with a renewed vision for preparation of the next generation of nursing scientists. Building on the 2005 National Research Council report Advancing The Nation's Health Needs and the 2010 American Association of Colleges of Nursing Position Statement on the Research-Focused Doctorate Pathways to Excellence, the IFAC specifically addressed the capacity of PhD programs to prepare nursing scientists to conduct cutting-edge research in the following key emerging and priority areas of health sciences research: omics and the microbiome; health behavior, behavior change, and biobehavioral science; patient-reported outcomes; big data, e-science, and informatics; quantitative sciences; translation science; and health economics. The purpose of this article is to (a) describe IFAC activities, (b) summarize 2014 discussions hosted as part of the Idea Festival, and (c) present IFAC recommendations for incorporating these emerging areas of science and technology into research-focused doctoral programs committed to preparing graduates for lifelong, competitive careers in nursing science. The recommendations address clearer articulation of program focus areas; inclusion of foundational knowledge in emerging areas of science in core courses on nursing science and research methods; faculty composition; prerequisite student knowledge and skills; and in-depth, interdisciplinary training in supporting area of science content and methods. Copyright © 2015 Elsevier Inc

  15. Multi-omic profiling of EPO producing Chinese hamster ovary cell panel reveals metabolic adaptation to heterologous protein production

    DEFF Research Database (Denmark)

    Ley, Daniel; Kazemi Seresht, Ali; Engmark, Mikael

    Heterologous protein production in CHO cells imposes a burden on the host cell metabolism and impact cellular physiology on a global scale. In this work, a multi-omics approach was applied to characterize the physiological impact of erythropoietin production, and discover production bottlenecks, ...

  16. "Omic" investigations of protozoa and worms for a deeper understanding of the human gut "parasitome".

    Science.gov (United States)

    Marzano, Valeria; Mancinelli, Livia; Bracaglia, Giorgia; Del Chierico, Federica; Vernocchi, Pamela; Di Girolamo, Francesco; Garrone, Stefano; Tchidjou Kuekou, Hyppolite; D'Argenio, Patrizia; Dallapiccola, Bruno; Urbani, Andrea; Putignani, Lorenza

    2017-11-01

    The human gut has been continuously exposed to a broad spectrum of intestinal organisms, including viruses, bacteria, fungi, and parasites (protozoa and worms), over millions of years of coevolution, and plays a central role in human health. The modern lifestyles of Western countries, such as the adoption of highly hygienic habits, the extensive use of antimicrobial drugs, and increasing globalisation, have dramatically altered the composition of the gut milieu, especially in terms of its eukaryotic "citizens." In the past few decades, numerous studies have highlighted the composition and role of human intestinal bacteria in physiological and pathological conditions, while few investigations exist on gut parasites and particularly on their coexistence and interaction with the intestinal microbiota. Studies of the gut "parasitome" through "omic" technologies, such as (meta)genomics, transcriptomics, proteomics, and metabolomics, are herein reviewed to better understand their role in the relationships between intestinal parasites, host, and resident prokaryotes, whether pathogens or commensals. Systems biology-based profiles of the gut "parasitome" under physiological and severe disease conditions can indeed contribute to the control of infectious diseases and offer a new perspective of omics-assisted tropical medicine.

  17. The emerging CHO systems biology era: harnessing the ‘omics revolution for biotechnology

    DEFF Research Database (Denmark)

    Kildegaard, Helene Faustrup; Baycin-Hizal, Deniz; Lewis, Nathan

    2013-01-01

    into mathematical models that describe CHO phenotypes will provide crucial biotechnology insights. As ‘omics technologies and computational systems biology mature, genome-scale approaches will lead to major innovations in cell line development and metabolic engineering, thereby improving protein production......Chinese hamster ovary (CHO) cells are the primary factories for biopharmaceuticals because of their capacity to correctly fold and post-translationally modify recombinant proteins compatible with humans. New opportunities are arising to enhance these cell factories, especially since the CHO-K1 cell...

  18. COMPUTATIONAL SCIENCE CENTER

    International Nuclear Information System (INIS)

    DAVENPORT, J.

    2006-01-01

    Computational Science is an integral component of Brookhaven's multi science mission, and is a reflection of the increased role of computation across all of science. Brookhaven currently has major efforts in data storage and analysis for the Relativistic Heavy Ion Collider (RHIC) and the ATLAS detector at CERN, and in quantum chromodynamics. The Laboratory is host for the QCDOC machines (quantum chromodynamics on a chip), 10 teraflop/s computers which boast 12,288 processors each. There are two here, one for the Riken/BNL Research Center and the other supported by DOE for the US Lattice Gauge Community and other scientific users. A 100 teraflop/s supercomputer will be installed at Brookhaven in the coming year, managed jointly by Brookhaven and Stony Brook, and funded by a grant from New York State. This machine will be used for computational science across Brookhaven's entire research program, and also by researchers at Stony Brook and across New York State. With Stony Brook, Brookhaven has formed the New York Center for Computational Science (NYCCS) as a focal point for interdisciplinary computational science, which is closely linked to Brookhaven's Computational Science Center (CSC). The CSC has established a strong program in computational science, with an emphasis on nanoscale electronic structure and molecular dynamics, accelerator design, computational fluid dynamics, medical imaging, parallel computing and numerical algorithms. We have been an active participant in DOES SciDAC program (Scientific Discovery through Advanced Computing). We are also planning a major expansion in computational biology in keeping with Laboratory initiatives. Additional laboratory initiatives with a dependence on a high level of computation include the development of hydrodynamics models for the interpretation of RHIC data, computational models for the atmospheric transport of aerosols, and models for combustion and for energy utilization. The CSC was formed to bring together

  19. Multi-omic profiling of EPO-producing Chinese hamster ovary cell panel reveals metabolic adaptation to heterologous protein production

    DEFF Research Database (Denmark)

    Ley, Daniel; Kazemi Seresht, Ali; Engmark, Mikael

    2015-01-01

    Chinese hamster ovary (CHO) cells are the preferred production host for many therapeutic proteins. The production of heterologous proteins in CHO cells imposes a burden on the host cell metabolism and impact cellular physiology on a global scale. In this work, a multi-omics approach was applied...

  20. Biochemical, physiological and molecular responses of Ricinus communis seeds and seedlings to different temperatures: a multi-omics approach

    NARCIS (Netherlands)

    Ribeiro de Jesus, P.R.

    2015-01-01

    Biochemical, physiological and molecular responses of Ricinus communis seeds and seedlings to different temperatures: a multi-omics approach

    by Paulo Roberto Ribeiro de Jesus

    The main objective of this thesis was to provide a detailed

  1. Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism.

    Science.gov (United States)

    Wallace, Robert J; Snelling, Timothy J; McCartney, Christine A; Tapio, Ilma; Strozzi, Francesco

    2017-01-16

    Methane emissions from ruminal fermentation contribute significantly to total anthropological greenhouse gas (GHG) emissions. New meta-omics technologies are beginning to revolutionise our understanding of the rumen microbial community structure, metabolic potential and metabolic activity. Here we explore these developments in relation to GHG emissions. Microbial rumen community analyses based on small subunit ribosomal RNA sequence analysis are not yet predictive of methane emissions from individual animals or treatments. Few metagenomics studies have been directly related to GHG emissions. In these studies, the main genes that differed in abundance between high and low methane emitters included archaeal genes involved in methanogenesis, with others that were not apparently related to methane metabolism. Unlike the taxonomic analysis up to now, the gene sets from metagenomes may have predictive value. Furthermore, metagenomic analysis predicts metabolic function better than only a taxonomic description, because different taxa share genes with the same function. Metatranscriptomics, the study of mRNA transcript abundance, should help to understand the dynamic of microbial activity rather than the gene abundance; to date, only one study has related the expression levels of methanogenic genes to methane emissions, where gene abundance failed to do so. Metaproteomics describes the proteins present in the ecosystem, and is therefore arguably a better indication of microbial metabolism. Both two-dimensional polyacrylamide gel electrophoresis and shotgun peptide sequencing methods have been used for ruminal analysis. In our unpublished studies, both methods showed an abundance of archaeal methanogenic enzymes, but neither was able to discriminate high and low emitters. Metabolomics can take several forms that appear to have predictive value for methane emissions; ruminal metabolites, milk fatty acid profiles, faecal long-chain alcohols and urinary metabolites have all

  2. [New-generation high-throughput technologies based 'omics' research strategy in human disease].

    Science.gov (United States)

    Yang, Xu; Jiao, Rui; Yang, Lin; Wu, Li-Ping; Li, Ying-Rui; Wang, Jun

    2011-08-01

    In recent years, new-generation high-throughput technologies, including next-generation sequencing technology and mass spectrometry method, have been widely applied in solving biological problems, especially in human diseases field. This data driven, large-scale and industrialized research model enables the omnidirectional and multi-level study of human diseases from the perspectives of genomics, transcriptomics and proteomics levels, etc. In this paper, the latest development of the high-throughput technologies that applied in DNA, RNA, epigenomics, metagenomics including proteomics and some applications in translational medicine are reviewed. At genomics level, exome sequencing has been the hot spot of the recent research. However, the predominance of whole genome resequencing in detecting large structural variants within the whole genome level is coming to stand out as the drop of sequencing cost, which also makes it possible for personalized genome based medicine application. At trancriptomics level, e.g., small RNA sequencing can be used to detect known and predict unknown miRNA. Those small RNA could not only be the biomarkers for disease diagnosis and prognosis, but also show the potential of disease treatment. At proteomics level, e.g., target proteomics can be used to detect the possible disease-related protein or peptides, which can be useful index for clinical staging and typing. Furthermore, the application and development of trans-omics study in disease research are briefly introduced. By applying bioinformatics technologies for integrating multi-omics data, the mechanism, diagnosis and therapy of the disease are likely to be systemically explained and realized, so as to provide powerful tools for disease diagnosis and therapies.

  3. COMICS: Cartoon Visualization of Omics Data in Spatial Context Using Anatomical Ontologies.

    Science.gov (United States)

    Travin, Dmitrii; Popov, Iaroslav; Guler, Arzu Tugce; Medvedev, Dmitry; van der Plas-Duivesteijn, Suzanne; Varela, Monica; Kolder, Iris C R M; Meijer, Annemarie H; Spaink, Herman P; Palmblad, Magnus

    2018-01-05

    COMICS is an interactive and open-access web platform for integration and visualization of molecular expression data in anatomograms of zebrafish, carp, and mouse model systems. Anatomical ontologies are used to map omics data across experiments and between an experiment and a particular visualization in a data-dependent manner. COMICS is built on top of several existing resources. Zebrafish and mouse anatomical ontologies with their controlled vocabulary (CV) and defined hierarchy are used with the ontoCAT R package to aggregate data for comparison and visualization. Libraries from the QGIS geographical information system are used with the R packages "maps" and "maptools" to visualize and interact with molecular expression data in anatomical drawings of the model systems. COMICS allows users to upload their own data from omics experiments, using any gene or protein nomenclature they wish, as long as CV terms are used to define anatomical regions or developmental stages. Common nomenclatures such as the ZFIN gene names and UniProt accessions are provided additional support. COMICS can be used to generate publication-quality visualizations of gene and protein expression across experiments. Unlike previous tools that have used anatomical ontologies to interpret imaging data in several animal models, including zebrafish, COMICS is designed to take spatially resolved data generated by dissection or fractionation and display this data in visually clear anatomical representations rather than large data tables. COMICS is optimized for ease-of-use, with a minimalistic web interface and automatic selection of the appropriate visual representation depending on the input data.

  4. Proceedings of RIKEN BNL Research Center workwhop on RHIC spin

    Energy Technology Data Exchange (ETDEWEB)

    SOFFER,J.

    1999-10-06

    This RHIC Spin Workshop is the 1999 annual meeting of the RHIC Spin Collaboration, and the second to be hosted at Brookhaven and sponsored by the RIKEN BNL Research Center. The previous meetings were at Brookhaven (1998), Marseille (1996), MIT in 1995, Argonne 1994, Tucson in 1991, and the Polarized Collider Workshop at Penn State in 1990. As noted last year, the Center provides a home for combined work on spin by theorists, experimenters, and accelerator physicists. This proceedings, as last year, is a compilation of 1 page summaries and 5 selected transparencies for each speaker. It is designed to be available soon after the workshop is completed. Speakers are welcome to include web or other references for additional material. The RHIC spin program and RHIC are rapidly becoming reality. RHIC has completed its first commissioning run, as described here by Steve Peggs. The first Siberian Snake for spin has been completed and is being installed in RHIC. A new polarized source from KEK and Triumf with over 1 milliampere of polarized H{sup minus} is being installed, described by Anatoli Zelenski. They have had a successful test of a new polarimeter for RHIC, described by Kazu Kurita and Haixin Huang. Spin commissioning is expected next spring (2000), and the first physics run for spin is anticipated for spring 2001. The purpose of the workshop is to get everyone together about once per year and discuss goals of the spin program, progress, problems, and new ideas. They also have many separate regular forums on spin. There are spin discussion sessions every Tuesday, now organized by Naohito Saito and Werner Vogelsang. The spin discussion schedule and copies of presentations are posted on http://riksg01.rhic.bnl.gov/rsc. Speakers and other spinners are encouraged to come to BNL and to lead a discussion on your favorite idea. They also have regular polarimeter and snake meetings on alternate Thursdays, led by Bill McGahern, the lead engineer for the accelerator spin

  5. Proceedings of RIKEN BNL Research Center workshop on RHIC spin

    International Nuclear Information System (INIS)

    Soffer, J.

    1999-01-01

    This RHIC Spin Workshop is the 1999 annual meeting of the RHIC Spin Collaboration, and the second to be hosted at Brookhaven and sponsored by the RIKEN BNL Research Center. The previous meetings were at Brookhaven (1998), Marseille (1996), MIT in 1995, Argonne 1994, Tucson in 1991, and the Polarized Collider Workshop at Penn State in 1990. As noted last year, the Center provides a home for combined work on spin by theorists, experimenters, and accelerator physicists. This proceedings, as last year, is a compilation of 1 page summaries and 5 selected transparencies for each speaker. It is designed to be available soon after the workshop is completed. Speakers are welcome to include web or other references for additional material. The RHIC spin program and RHIC are rapidly becoming reality. RHIC has completed its first commissioning run, as described here by Steve Peggs. The first Siberian Snake for spin has been completed and is being installed in RHIC. A new polarized source from KEK and Triumf with over 1 milliampere of polarized H minus is being installed, described by Anatoli Zelenski. They have had a successful test of a new polarimeter for RHIC, described by Kazu Kurita and Haixin Huang. Spin commissioning is expected next spring (2000), and the first physics run for spin is anticipated for spring 2001. The purpose of the workshop is to get everyone together about once per year and discuss goals of the spin program, progress, problems, and new ideas. They also have many separate regular forums on spin. There are spin discussion sessions every Tuesday, now organized by Naohito Saito and Werner Vogelsang. The spin discussion schedule and copies of presentations are posted on http://riksg01.rhic.bnl.gov/rsc. Speakers and other spinners are encouraged to come to BNL and to lead a discussion on your favorite idea. They also have regular polarimeter and snake meetings on alternate Thursdays, led by Bill McGahern, the lead engineer for the accelerator spin effort

  6. ShockOmics: multiscale approach to the identification of molecular biomarkers in acute heart failure induced by shock.

    Science.gov (United States)

    Aletti, Federico; Conti, Costanza; Ferrario, Manuela; Ribas, Vicent; Bollen Pinto, Bernardo; Herpain, Antoine; Post, Emiel; Romay Medina, Eduardo; Barlassina, Cristina; de Oliveira, Eliandre; Pastorelli, Roberta; Tedeschi, Gabriella; Ristagno, Giuseppe; Taccone, Fabio S; Schmid-Schönbein, Geert W; Ferrer, Ricard; De Backer, Daniel; Bendjelid, Karim; Baselli, Giuseppe

    2016-01-28

    The ShockOmics study (ClinicalTrials.gov identifier NCT02141607) is a multicenter prospective observational trial aimed at identifying new biomarkers of acute heart failure in circulatory shock, by means of a multiscale analysis of blood samples and hemodynamic data from subjects with circulatory shock. Ninety septic shock and cardiogenic shock patients will be recruited in three intensive care units (ICU) (Hôpital Erasme, Université Libre de Bruxelles, Belgium; Hospital Universitari Mutua Terrassa, Spain; Hôpitaux Universitaires de Genève, Switzerland). Hemodynamic signals will be recorded every day for up to seven days from shock diagnosis (time T0). Clinical data and blood samples will be collected for analysis at: i) T1  5 and lactate levels ≥ 2 mmol/L. The exclusion criteria are: expected death within 24 h since ICU admission; > 4 units of red blood cells or >1 fresh frozen plasma transfused; active hematological malignancy; metastatic cancer; chronic immunodepression; pre-existing end stage renal disease requiring renal replacement therapy; recent cardiac surgery; Child-Pugh C cirrhosis; terminal illness. Enrollment will be preceded by the signature of the Informed Consent by the patient or his/her relatives and by the physician in charge. Three non-shock control groups will be included in the study: a) healthy blood donors (n = 5); b) septic patients (n = 10); c) acute myocardial infarction or patients with prolonged acute arrhythmia (n = 10). The hemodynamic data will be downloaded from the ICU monitors by means of dedicated software. The blood samples will be utilized for transcriptomics, proteomics and metabolomics ("-omics") analyses. ShockOmics will provide new insights into the pathophysiological mechanisms underlying shock as well as new biomarkers for the timely diagnosis of cardiac dysfunction in shock and quantitative indices for assisting the therapeutic management of shock patients.

  7. Omics analysis of human bone to identify genes and molecular networks regulating skeletal remodeling in health and disease.

    Science.gov (United States)

    Reppe, Sjur; Datta, Harish K; Gautvik, Kaare M

    2017-08-01

    The skeleton is a metabolically active organ throughout life where specific bone cell activity and paracrine/endocrine factors regulate its morphogenesis and remodeling. In recent years, an increasing number of reports have used multi-omics technologies to characterize subsets of bone biological molecular networks. The skeleton is affected by primary and secondary disease, lifestyle and many drugs. Therefore, to obtain relevant and reliable data from well characterized patient and control cohorts are vital. Here we provide a brief overview of omics studies performed on human bone, of which our own studies performed on trans-iliacal bone biopsies from postmenopausal women with osteoporosis (OP) and healthy controls are among the first and largest. Most other studies have been performed on smaller groups of patients, undergoing hip replacement for osteoarthritis (OA) or fracture, and without healthy controls. The major findings emerging from the combined studies are: 1. Unstressed and stressed bone show profoundly different gene expression reflecting differences in bone turnover and remodeling and 2. Omics analyses comparing healthy/OP and control/OA cohorts reveal characteristic changes in transcriptomics, epigenomics (DNA methylation), proteomics and metabolomics. These studies, together with genome-wide association studies, in vitro observations and transgenic animal models have identified a number of genes and gene products that act via Wnt and other signaling systems and are highly associated to bone density and fracture. Future challenge is to understand the functional interactions between bone-related molecular networks and their significance in OP and OA pathogenesis, and also how the genomic architecture is affected in health and disease. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. A Concise Review on Multi-Omics Data Integration for Terroir Analysis in Vitis vinifera

    Directory of Open Access Journals (Sweden)

    Pastor Jullian Fabres

    2017-06-01

    Full Text Available Vitis vinifera (grapevine is one of the most important fruit crops, both for fresh consumption and wine and spirit production. The term terroir is frequently used in viticulture and the wine industry to relate wine sensory attributes to its geographic origin. Although, it can be cultivated in a wide range of environments, differences in growing conditions have a significant impact on fruit traits that ultimately affect wine quality. Understanding how fruit quality and yield are controlled at a molecular level in grapevine in response to environmental cues has been a major driver of research. Advances in the area of genomics, epigenomics, transcriptomics, proteomics and metabolomics, have significantly increased our knowledge on the abiotic regulation of yield and quality in many crop species, including V. vinifera. The integrated analysis of multiple ‘omics’ can give us the opportunity to better understand how plants modulate their response to different environments. However, ‘omics’ technologies provide a large amount of biological data and its interpretation is not always straightforward, especially when different ‘omic’ results are combined. Here we examine the current strategies used to integrate multi-omics, and how these have been used in V. vinifera. In addition, we also discuss the importance of including epigenomics data when integrating omics data as epigenetic mechanisms could play a major role as an intermediary between the environment and the genome.

  9. Exploring Omics data from designed experiments using analysis of variance multiblock Orthogonal Partial Least Squares

    International Nuclear Information System (INIS)

    Boccard, Julien; Rudaz, Serge

    2016-01-01

    Many experimental factors may have an impact on chemical or biological systems. A thorough investigation of the potential effects and interactions between the factors is made possible by rationally planning the trials using systematic procedures, i.e. design of experiments. However, assessing factors' influences remains often a challenging task when dealing with hundreds to thousands of correlated variables, whereas only a limited number of samples is available. In that context, most of the existing strategies involve the ANOVA-based partitioning of sources of variation and the separate analysis of ANOVA submatrices using multivariate methods, to account for both the intrinsic characteristics of the data and the study design. However, these approaches lack the ability to summarise the data using a single model and remain somewhat limited for detecting and interpreting subtle perturbations hidden in complex Omics datasets. In the present work, a supervised multiblock algorithm based on the Orthogonal Partial Least Squares (OPLS) framework, is proposed for the joint analysis of ANOVA submatrices. This strategy has several advantages: (i) the evaluation of a unique multiblock model accounting for all sources of variation; (ii) the computation of a robust estimator (goodness of fit) for assessing the ANOVA decomposition reliability; (iii) the investigation of an effect-to-residuals ratio to quickly evaluate the relative importance of each effect and (iv) an easy interpretation of the model with appropriate outputs. Case studies from metabolomics and transcriptomics, highlighting the ability of the method to handle Omics data obtained from fixed-effects full factorial designs, are proposed for illustration purposes. Signal variations are easily related to main effects or interaction terms, while relevant biochemical information can be derived from the models. - Highlights: • A new method is proposed for the analysis of Omics data generated using design of experiments

  10. Exploring Omics data from designed experiments using analysis of variance multiblock Orthogonal Partial Least Squares

    Energy Technology Data Exchange (ETDEWEB)

    Boccard, Julien, E-mail: julien.boccard@unige.ch; Rudaz, Serge

    2016-05-12

    Many experimental factors may have an impact on chemical or biological systems. A thorough investigation of the potential effects and interactions between the factors is made possible by rationally planning the trials using systematic procedures, i.e. design of experiments. However, assessing factors' influences remains often a challenging task when dealing with hundreds to thousands of correlated variables, whereas only a limited number of samples is available. In that context, most of the existing strategies involve the ANOVA-based partitioning of sources of variation and the separate analysis of ANOVA submatrices using multivariate methods, to account for both the intrinsic characteristics of the data and the study design. However, these approaches lack the ability to summarise the data using a single model and remain somewhat limited for detecting and interpreting subtle perturbations hidden in complex Omics datasets. In the present work, a supervised multiblock algorithm based on the Orthogonal Partial Least Squares (OPLS) framework, is proposed for the joint analysis of ANOVA submatrices. This strategy has several advantages: (i) the evaluation of a unique multiblock model accounting for all sources of variation; (ii) the computation of a robust estimator (goodness of fit) for assessing the ANOVA decomposition reliability; (iii) the investigation of an effect-to-residuals ratio to quickly evaluate the relative importance of each effect and (iv) an easy interpretation of the model with appropriate outputs. Case studies from metabolomics and transcriptomics, highlighting the ability of the method to handle Omics data obtained from fixed-effects full factorial designs, are proposed for illustration purposes. Signal variations are easily related to main effects or interaction terms, while relevant biochemical information can be derived from the models. - Highlights: • A new method is proposed for the analysis of Omics data generated using design of

  11. NUMERICAL ALGORITHMS AT NON-ZERO CHEMICAL POTENTIAL. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP, VOLUME 19

    International Nuclear Information System (INIS)

    Blum, T.; Creutz, M.

    1999-01-01

    The RIKEN BNL Research Center hosted its 19th workshop April 27th through May 1, 1999. The topic was Numerical Algorithms at Non-Zero Chemical Potential. QCD at a non-zero chemical potential (non-zero density) poses a long-standing unsolved challenge for lattice gauge theory. Indeed, it is the primary unresolved issue in the fundamental formulation of lattice gauge theory. The chemical potential renders conventional lattice actions complex, practically excluding the usual Monte Carlo techniques which rely on a positive definite measure for the partition function. This ''sign'' problem appears in a wide range of physical systems, ranging from strongly coupled electronic systems to QCD. The lack of a viable numerical technique at non-zero density is particularly acute since new exotic ''color superconducting'' phases of quark matter have recently been predicted in model calculations. A first principles confirmation of the phase diagram is desirable since experimental verification is not expected soon. At the workshop several proposals for new algorithms were made: cluster algorithms, direct simulation of Grassman variables, and a bosonization of the fermion determinant. All generated considerable discussion and seem worthy of continued investigation. Several interesting results using conventional algorithms were also presented: condensates in four fermion models, SU(2) gauge theory in fundamental and adjoint representations, and lessons learned from strong; coupling, non-zero temperature and heavy quarks applied to non-zero density simulations

  12. Pramana – Journal of Physics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Physics Department, University of Tokyo, Tokyo 113-0033, Japan; RIKEN BNL Research Center, Brookhaven National Laboratory, Upton, NY 11973, USA; Department of Physics, Waseda University, Tokyo 169-8555, Japan; Tokuyama Women's College, Tokuyama, Yamaguchi 745-8511, Japan; IMC, Hiroshima University, ...

  13. COMPUTATIONAL SCIENCE CENTER

    Energy Technology Data Exchange (ETDEWEB)

    DAVENPORT, J.

    2006-11-01

    Computational Science is an integral component of Brookhaven's multi science mission, and is a reflection of the increased role of computation across all of science. Brookhaven currently has major efforts in data storage and analysis for the Relativistic Heavy Ion Collider (RHIC) and the ATLAS detector at CERN, and in quantum chromodynamics. The Laboratory is host for the QCDOC machines (quantum chromodynamics on a chip), 10 teraflop/s computers which boast 12,288 processors each. There are two here, one for the Riken/BNL Research Center and the other supported by DOE for the US Lattice Gauge Community and other scientific users. A 100 teraflop/s supercomputer will be installed at Brookhaven in the coming year, managed jointly by Brookhaven and Stony Brook, and funded by a grant from New York State. This machine will be used for computational science across Brookhaven's entire research program, and also by researchers at Stony Brook and across New York State. With Stony Brook, Brookhaven has formed the New York Center for Computational Science (NYCCS) as a focal point for interdisciplinary computational science, which is closely linked to Brookhaven's Computational Science Center (CSC). The CSC has established a strong program in computational science, with an emphasis on nanoscale electronic structure and molecular dynamics, accelerator design, computational fluid dynamics, medical imaging, parallel computing and numerical algorithms. We have been an active participant in DOES SciDAC program (Scientific Discovery through Advanced Computing). We are also planning a major expansion in computational biology in keeping with Laboratory initiatives. Additional laboratory initiatives with a dependence on a high level of computation include the development of hydrodynamics models for the interpretation of RHIC data, computational models for the atmospheric transport of aerosols, and models for combustion and for energy utilization. The CSC was formed to

  14. A 'Foodomic' Approach for the Evaluation of Food Quality and its Impact on the Human Metabolome

    DEFF Research Database (Denmark)

    Trimigno, Alessia

    In recent years, omic sciences have been increasingly employed in a multitude of research fields thanks to their high-throughput capabilities and holistic approach. Among the omic sciences, metabolomics and foodomics have recently emerged in the investigation of food and nutrition and their relat......In recent years, omic sciences have been increasingly employed in a multitude of research fields thanks to their high-throughput capabilities and holistic approach. Among the omic sciences, metabolomics and foodomics have recently emerged in the investigation of food and nutrition...... and their relation to the individual health and wellness status (Chapter 1). The analytical platforms used are ideal for non-targeted analysis, due to their capability of detecting and identifying a large set of variables (or metabolites) in complex biological samples. The most employed metabolomics techniques...... carried out both in Italy and in Denmark, outlines the analytical pipeline of the foodomic approach and highlights the current challenges in the field (Chapter 2.3). The thesis traces the path of modern foodomics and metabolomics from the definition and description of food quality (Chapters 3 to 6...

  15. [Nutrigenetics and nutrigenomics - application of „omics” technologies in optimization of human nutrition].

    Science.gov (United States)

    Panczyk, Mariusz

    2013-01-01

    Nowadays nutrigenetics and nutrigenomics are perceived as one of the most important research areas ensuring better understanding of an impact of nutrition on human health. Since such researches are interdisciplinary in type, there is a problem with their widespread acceptance and practical clinical application of obtained results. Understanding the new ideas and hypotheses published in researches on nutrigenetics/nutrigenomics requires some knowledge of genetics, biochemistry, molecular biology, and capabilities and limitations that are associated with the use of statistical and bioinformatic analysis, and above all „omics” research technologies (genomics, transcriptomics, proteomics, metabolomics). Highly efficient genome and proteome analysis techniques allow to obtain data necessary for profiling of an individual patient. The main problem is still our insufficient knowledge of cell physiology and biochemistry. The vast amount of information is obtained with the use of „omics” technologies what makes it difficult to interpret and infer. An unquestionable advantage of this type of research is the possibility to utilize system analysis (system biology) which is important in the context of a holistic interpretation of biological phenomena. This review is an attempt to present the main hypotheses and objectives which are carried out by researchers in nutrigenetics/nutrigenomics. This article describes the most important directions of research and anticipated results that are related to the practical use of nutritional genomics as well as the critical assessment of the possible impact of future developments on public health.

  16. "Polymeromics": Mass spectrometry based strategies in polymer science toward complete sequencing approaches: a review.

    Science.gov (United States)

    Altuntaş, Esra; Schubert, Ulrich S

    2014-01-15

    Mass spectrometry (MS) is the most versatile and comprehensive method in "OMICS" sciences (i.e. in proteomics, genomics, metabolomics and lipidomics). The applications of MS and tandem MS (MS/MS or MS(n)) provide sequence information of the full complement of biological samples in order to understand the importance of the sequences on their precise and specific functions. Nowadays, the control of polymer sequences and their accurate characterization is one of the significant challenges of current polymer science. Therefore, a similar approach can be very beneficial for characterizing and understanding the complex structures of synthetic macromolecules. MS-based strategies allow a relatively precise examination of polymeric structures (e.g. their molar mass distributions, monomer units, side chain substituents, end-group functionalities, and copolymer compositions). Moreover, tandem MS offer accurate structural information from intricate macromolecular structures; however, it produces vast amount of data to interpret. In "OMICS" sciences, the software application to interpret the obtained data has developed satisfyingly (e.g. in proteomics), because it is not possible to handle the amount of data acquired via (tandem) MS studies on the biological samples manually. It can be expected that special software tools will improve the interpretation of (tandem) MS output from the investigations of synthetic polymers as well. Eventually, the MS/MS field will also open up for polymer scientists who are not MS-specialists. In this review, we dissect the overall framework of the MS and MS/MS analysis of synthetic polymers into its key components. We discuss the fundamentals of polymer analyses as well as recent advances in the areas of tandem mass spectrometry, software developments, and the overall future perspectives on the way to polymer sequencing, one of the last Holy Grail in polymer science. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Omics techniques and biobanks to find new biomarkers for the early detection of acute lymphoblastic leukemia in middle-income countries: a perspective from Mexico.

    Science.gov (United States)

    Aguirre-Guillén, William Alejandro; Angeles-Floriano, Tania; López-Martínez, Briceida; Reyes-Morales, Hortensia; Zlotnik, Albert; Valle-Rios, Ricardo

    Acute lymphoblastic leukemia (ALL) affects the quality of life of many children in the world and particularly in Mexico, where a high incidence has been reported. With a proper financial investment and with well-organized institutions caring for those patients, together with solid platforms to perform high-throughput analyses, we propose the creation of a Mexican repository system of serum and cells from bone marrow and blood samples derived from tissues of pediatric patients with ALL diagnosis. This resource, in combination with omics technologies, particularly proteomics and metabolomics, would allow longitudinal studies, offering an opportunity to design and apply personalized ALL treatments. Importantly, it would accelerate the development of translational science and will lead us to further discoveries, including the identification of new biomarkers for the early detection of leukemia. Copyright © 2017 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

  18. Omics-based approaches reveal phospholipids remodeling of Rhizopus oryzae responding to furfural stress for fumaric acid-production from xylose.

    Science.gov (United States)

    Pan, Xinrong; Liu, Huanhuan; Liu, Jiao; Wang, Cheng; Wen, Jianping

    2016-12-01

    In order to relieve the toxicity of furfural on Rhizopus oryzae fermentation, the molecular mechanism of R. oryzae responding to furfural stress for fumaric acid-production was investigated by omics-based approaches. In metabolomics analysis, 29 metabolites including amino acid, sugars, polyols and fatty acids showed significant changes for maintaining the basic cell metabolism at the cost of lowering fumaric acid production. To further uncover the survival mechanism, lipidomics was carried out, revealing that phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and polyunsaturated acyl chains might be closely correlated with R. oryzae's adapting to furfural stress. Based on the above omics analysis, lecithin, inositol and soybean oil were exogenously supplemented separately with an optimized concentration in the presence of furfural, which increased fumaric acid titer from 5.78g/L to 10.03g/L, 10.05g/L and 12.13g/L (increased by 73.5%, 73.8% and 110%, respectively). These findings provide a methodological guidance for hemicellulose-fumaric acid development. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer.

    Directory of Open Access Journals (Sweden)

    Matthew Ruffalo

    2015-12-01

    Full Text Available Development of high-throughput monitoring technologies enables interrogation of cancer samples at various levels of cellular activity. Capitalizing on these developments, various public efforts such as The Cancer Genome Atlas (TCGA generate disparate omic data for large patient cohorts. As demonstrated by recent studies, these heterogeneous data sources provide the opportunity to gain insights into the molecular changes that drive cancer pathogenesis and progression. However, these insights are limited by the vast search space and as a result low statistical power to make new discoveries. In this paper, we propose methods for integrating disparate omic data using molecular interaction networks, with a view to gaining mechanistic insights into the relationship between molecular changes at different levels of cellular activity. Namely, we hypothesize that genes that play a role in cancer development and progression may be implicated by neither frequent mutation nor differential expression, and that network-based integration of mutation and differential expression data can reveal these "silent players". For this purpose, we utilize network-propagation algorithms to simulate the information flow in the cell at a sample-specific resolution. We then use the propagated mutation and expression signals to identify genes that are not necessarily mutated or differentially expressed genes, but have an essential role in tumor development and patient outcome. We test the proposed method on breast cancer and glioblastoma multiforme data obtained from TCGA. Our results show that the proposed method can identify important proteins that are not readily revealed by molecular data, providing insights beyond what can be gleaned by analyzing different types of molecular data in isolation.

  20. Material science as basis for nuclear medicine: Holmium irradiation for radioisotopes production

    Science.gov (United States)

    Usman, Ahmed Rufai; Khandaker, Mayeen Uddin; Haba, Hiromitsu; Otuka, Naohiko

    2018-05-01

    Material Science, being an interdisciplinary field, plays important roles in nuclear science. These applications are seen in weaponry, armoured vehicles, accelerator structure and development, semiconductor detectors, nuclear medicine and many more. Present study presents the applications of some metals in nuclear medicine (radioisotope production). The charged-particle-induced nuclear reactions by using cyclotrons or accelerators have become a very vital feature of the modern nuclear medicine. Realising the importance of excitation functions for the efficient production of medical radionuclides, some very high purity holmium metals are generally prepared or purchased for bombardment in nuclear accelerators. In the present work, various methods to obtain pure holmium for radioisotope production have been discussed while also presenting details of our present studies. From the experimental work of the present studies, some very high purity holmium foils have been used in the work for a comprehensive study of residual radionuclides production cross-sections. The study was performed using a stacked-foil activation technique combined with γ-ray spectrometry. The stack was bombarded with 50.4 MeV alpha particle beam from AVF cyclotron of RI Beam Factory, Nishina Centre for Accelerator-Based Science, RIKEN, Japan. The work produced thulium radionuclides useful in nuclear medicine.

  1. IPF-LASSO: Integrative L1-Penalized Regression with Penalty Factors for Prediction Based on Multi-Omics Data

    Directory of Open Access Journals (Sweden)

    Anne-Laure Boulesteix

    2017-01-01

    Full Text Available As modern biotechnologies advance, it has become increasingly frequent that different modalities of high-dimensional molecular data (termed “omics” data in this paper, such as gene expression, methylation, and copy number, are collected from the same patient cohort to predict the clinical outcome. While prediction based on omics data has been widely studied in the last fifteen years, little has been done in the statistical literature on the integration of multiple omics modalities to select a subset of variables for prediction, which is a critical task in personalized medicine. In this paper, we propose a simple penalized regression method to address this problem by assigning different penalty factors to different data modalities for feature selection and prediction. The penalty factors can be chosen in a fully data-driven fashion by cross-validation or by taking practical considerations into account. In simulation studies, we compare the prediction performance of our approach, called IPF-LASSO (Integrative LASSO with Penalty Factors and implemented in the R package ipflasso, with the standard LASSO and sparse group LASSO. The use of IPF-LASSO is also illustrated through applications to two real-life cancer datasets. All data and codes are available on the companion website to ensure reproducibility.

  2. Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants.

    Science.gov (United States)

    Großkinsky, Dominik K; Syaifullah, Syahnada Jaya; Roitsch, Thomas

    2018-02-12

    The study of senescence in plants is complicated by diverse levels of temporal and spatial dynamics as well as the impact of external biotic and abiotic factors and crop plant management. Whereas the molecular mechanisms involved in developmentally regulated leaf senescence are very well understood, in particular in the annual model plant species Arabidopsis, senescence of other organs such as the flower, fruit, and root is much less studied as well as senescence in perennials such as trees. This review addresses the need for the integration of multi-omics techniques and physiological phenotyping into holistic phenomics approaches to dissect the complex phenomenon of senescence. That became feasible through major advances in the establishment of various, complementary 'omics' technologies. Such an interdisciplinary approach will also need to consider knowledge from the animal field, in particular in relation to novel regulators such as small, non-coding RNAs, epigenetic control and telomere length. Such a characterization of phenotypes via the acquisition of high-dimensional datasets within a systems biology approach will allow us to systematically characterize the various programmes governing senescence beyond leaf senescence in Arabidopsis and to elucidate the underlying molecular processes. Such a multi-omics approach is expected to also spur the application of results from model plants to agriculture and their verification for sustainable and environmentally friendly improvement of crop plant stress resilience and productivity and contribute to improvements based on postharvest physiology for the food industry and the benefit of its customers. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  3. Post-genomics nanotechnology is gaining momentum: nanoproteomics and applications in life sciences.

    Science.gov (United States)

    Kobeissy, Firas H; Gulbakan, Basri; Alawieh, Ali; Karam, Pierre; Zhang, Zhiqun; Guingab-Cagmat, Joy D; Mondello, Stefania; Tan, Weihong; Anagli, John; Wang, Kevin

    2014-02-01

    The post-genomics era has brought about new Omics biotechnologies, such as proteomics and metabolomics, as well as their novel applications to personal genomics and the quantified self. These advances are now also catalyzing other and newer post-genomics innovations, leading to convergences between Omics and nanotechnology. In this work, we systematically contextualize and exemplify an emerging strand of post-genomics life sciences, namely, nanoproteomics and its applications in health and integrative biological systems. Nanotechnology has been utilized as a complementary component to revolutionize proteomics through different kinds of nanotechnology applications, including nanoporous structures, functionalized nanoparticles, quantum dots, and polymeric nanostructures. Those applications, though still in their infancy, have led to several highly sensitive diagnostics and new methods of drug delivery and targeted therapy for clinical use. The present article differs from previous analyses of nanoproteomics in that it offers an in-depth and comparative evaluation of the attendant biotechnology portfolio and their applications as seen through the lens of post-genomics life sciences and biomedicine. These include: (1) immunosensors for inflammatory, pathogenic, and autoimmune markers for infectious and autoimmune diseases, (2) amplified immunoassays for detection of cancer biomarkers, and (3) methods for targeted therapy and automatically adjusted drug delivery such as in experimental stroke and brain injury studies. As nanoproteomics becomes available both to the clinician at the bedside and the citizens who are increasingly interested in access to novel post-genomics diagnostics through initiatives such as the quantified self, we anticipate further breakthroughs in personalized and targeted medicine.

  4. Stemcell Information: SKIP000811 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available day No 5% ... RIKEN BioResouce Center (RIKEN ... BRC) 理化学研究所バイオリソースセンター RIKEN BioResouce Center (RIKEN ... BRC) 理化学...研究所バイオリソースセンター Available RIKEN BioResouce Center (RIKEN ... BRC) 理化学

  5. Stemcell Information: SKIP000809 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available Negative ... RIKEN BioResouce Center (RIKEN ... BRC) 理化学研究所バイオリ...ソースセンター RIKEN BioResouce Center (RIKEN ... BRC) 理化学研究所バイオリソースセンター Available RIKEN BioResouce Center (RIKEN ... BRC) 理化学

  6. Stemcell Information: SKIP000810 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available No 5% ... RIKEN BioResouce Center (RIKEN ... BRC) 理化学研究所バイオリソースセンター RIKEN BioResouce Center (RIKEN ... BRC) 理化学...研究所バイオリソースセンター Available RIKEN BioResouce Center (RIKEN ... BRC) 理化学

  7. Profiling microbial lignocellulose degradation and utilization by emergent omics technologies.

    Science.gov (United States)

    Rosnow, Joshua J; Anderson, Lindsey N; Nair, Reji N; Baker, Erin S; Wright, Aaron T

    2017-08-01

    The use of plant materials to generate renewable biofuels and other high-value chemicals is the sustainable and preferable option, but will require considerable improvements to increase the rate and efficiency of lignocellulose depolymerization. This review highlights novel and emerging technologies that are being developed and deployed to characterize the process of lignocellulose degradation. The review will also illustrate how microbial communities deconstruct and metabolize lignocellulose by identifying the necessary genes and enzyme activities along with the reaction products. These technologies include multi-omic measurements, cell sorting and isolation, nuclear magnetic resonance spectroscopy (NMR), activity-based protein profiling, and direct measurement of enzyme activity. The recalcitrant nature of lignocellulose necessitates the need to characterize the methods microbes employ to deconstruct lignocellulose to inform new strategies on how to greatly improve biofuel conversion processes. New technologies are yielding important insights into microbial functions and strategies employed to degrade lignocellulose, providing a mechanistic blueprint in order to advance biofuel production.

  8. The information science of microbial ecology.

    Science.gov (United States)

    Hahn, Aria S; Konwar, Kishori M; Louca, Stilianos; Hanson, Niels W; Hallam, Steven J

    2016-06-01

    A revolution is unfolding in microbial ecology where petabytes of 'multi-omics' data are produced using next generation sequencing and mass spectrometry platforms. This cornucopia of biological information has enormous potential to reveal the hidden metabolic powers of microbial communities in natural and engineered ecosystems. However, to realize this potential, the development of new technologies and interpretative frameworks grounded in ecological design principles are needed to overcome computational and analytical bottlenecks. Here we explore the relationship between microbial ecology and information science in the era of cloud-based computation. We consider microorganisms as individual information processing units implementing a distributed metabolic algorithm and describe developments in ecoinformatics and ubiquitous computing with the potential to eliminate bottlenecks and empower knowledge creation and translation. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. Cross-study and cross-omics comparisons of three nephrotoxic compounds reveal mechanistic insights and new candidate biomarkers

    International Nuclear Information System (INIS)

    Matheis, Katja A.; Com, Emmanuelle; Gautier, Jean-Charles; Guerreiro, Nelson; Brandenburg, Arnd; Gmuender, Hans; Sposny, Alexandra; Hewitt, Philip; Amberg, Alexander; Boernsen, Olaf; Riefke, Bjoern; Hoffmann, Dana; Mally, Angela; Kalkuhl, Arno; Suter, Laura; Dieterle, Frank; Staedtler, Frank

    2011-01-01

    The European InnoMed-PredTox project was a collaborative effort between 15 pharmaceutical companies, 2 small and mid-sized enterprises, and 3 universities with the goal of delivering deeper insights into the molecular mechanisms of kidney and liver toxicity and to identify mechanism-linked diagnostic or prognostic safety biomarker candidates by combining conventional toxicological parameters with 'omics' data. Mechanistic toxicity studies with 16 different compounds, 2 dose levels, and 3 time points were performed in male Crl: WI(Han) rats. Three of the 16 investigated compounds, BI-3 (FP007SE), Gentamicin (FP009SF), and IMM125 (FP013NO), induced kidney proximal tubule damage (PTD). In addition to histopathology and clinical chemistry, transcriptomics microarray and proteomics 2D-DIGE analysis were performed. Data from the three PTD studies were combined for a cross-study and cross-omics meta-analysis of the target organ. The mechanistic interpretation of kidney PTD-associated deregulated transcripts revealed, in addition to previously described kidney damage transcript biomarkers such as KIM-1, CLU and TIMP-1, a number of additional deregulated pathways congruent with histopathology observations on a single animal basis, including a specific effect on the complement system. The identification of new, more specific biomarker candidates for PTD was most successful when transcriptomics data were used. Combining transcriptomics data with proteomics data added extra value.

  10. A systemic identification approach for primary transcription start site of Arabidopsis miRNAs from multidimensional omics data.

    Science.gov (United States)

    You, Qi; Yan, Hengyu; Liu, Yue; Yi, Xin; Zhang, Kang; Xu, Wenying; Su, Zhen

    2017-05-01

    The 22-nucleotide non-coding microRNAs (miRNAs) are mostly transcribed by RNA polymerase II and are similar to protein-coding genes. Unlike the clear process from stem-loop precursors to mature miRNAs, the primary transcriptional regulation of miRNA, especially in plants, still needs to be further clarified, including the original transcription start site, functional cis-elements and primary transcript structures. Due to several well-characterized transcription signals in the promoter region, we proposed a systemic approach integrating multidimensional "omics" (including genomics, transcriptomics, and epigenomics) data to improve the genome-wide identification of primary miRNA transcripts. Here, we used the model plant Arabidopsis thaliana to improve the ability to identify candidate promoter locations in intergenic miRNAs and to determine rules for identifying primary transcription start sites of miRNAs by integrating high-throughput omics data, such as the DNase I hypersensitive sites, chromatin immunoprecipitation-sequencing of polymerase II and H3K4me3, as well as high throughput transcriptomic data. As a result, 93% of refined primary transcripts could be confirmed by the primer pairs from a previous study. Cis-element and secondary structure analyses also supported the feasibility of our results. This work will contribute to the primary transcriptional regulatory analysis of miRNAs, and the conserved regulatory pattern may be a suitable miRNA characteristic in other plant species.

  11. Evaluating the antidiabetic effects of Chinese herbal medicine: Xiao-Ke-An in 3T3-L1 cells and KKAy mice using both conventional and holistic omics approaches.

    Science.gov (United States)

    Yang, Zhenzhong; Wang, Linli; Zhang, Feng; Li, Zheng

    2015-08-13

    Xiao-Ke-An (XKA) is a Chinese medicine widely used for treating type 2 diabetes mellitus (T2D). It is composed of eight herbal medicines traditionally used for T2D, including Rehmannia glutinosa Libosch, Anemarrhena asphodeloides Bunge, Coptis chinensis Franch, etc. The aim of the present study was to investigate the antidiabetic effects of XKA with both conventional and holistic omics approaches. The antidiabetic effect of XKA was first investigated in 3T3-L1 cells to study the effect of XKA on adipogenesis in vitro. Oil Red O staining was performed to determine the lipid accumulation. The intracellular total cholesterol (TC) and triglyceride (TG) contents in XKA treated 3T3-L1 cells were also evaluated. The therapeutic effects of XKA was further evaluated in KKAy mice with both conventional and holistic omics approaches. Body weight, fasting and non-fasting blood glucose, and oral glucose tolerance were measured during the experiment. At the time of sacrifice, serum was collected for the measurement of TG, TC, high-density lipoprotein cholesterol (HDL-c) and low-density lipoprotein cholesterol (LDL-c). The liver, kidney, spleen, pancreas, heart and adipose tissues were harvested and weighted. The liver was used for further microarray experiment. Omics approaches were adopted to evaluate the holistic rebalancing effect of XKA at molecular network level. XKA significantly inhibited adipogenic differentiation, lowered the intracellular TC and TG contents in 3T3-L1 cells. XKA improved the glucose homeostasis and lipid metabolism, ameliorated insulin resistance in KKAy mice. Furthermore, XKA also exhibited effective therapeutic effects by reversing the molecular T2D disease network from an unbalanced state. This study investigated the antidiabetic effects of XKA with both conventional and holistic omics approaches, providing both phenotypic evidence and underlying action mechanisms for the clinical use of XKA treating T2D.

  12. Stemcell Information: SKIP000808 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ... RIKEN BioResouce Center (RIKEN ... BRC) 理化学研究所バイオリソースセンター RIKEN BioResouce Center (RIKEN ... BRC) 理化学...研究所バイオリソースセンター Available RIKEN BioResouce Center (RIKEN ... BRC) 理化学研究所バイオリソースセンター http://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HPS0136&type=1 ...

  13. Statistical analysis of proteomics, metabolomics, and lipidomics data using mass spectrometry

    CERN Document Server

    Mertens, Bart

    2017-01-01

    This book presents an overview of computational and statistical design and analysis of mass spectrometry-based proteomics, metabolomics, and lipidomics data. This contributed volume provides an introduction to the special aspects of statistical design and analysis with mass spectrometry data for the new omic sciences. The text discusses common aspects of design and analysis between and across all (or most) forms of mass spectrometry, while also providing special examples of application with the most common forms of mass spectrometry. Also covered are applications of computational mass spectrometry not only in clinical study but also in the interpretation of omics data in plant biology studies. Omics research fields are expected to revolutionize biomolecular research by the ability to simultaneously profile many compounds within either patient blood, urine, tissue, or other biological samples. Mass spectrometry is one of the key analytical techniques used in these new omic sciences. Liquid chromatography mass ...

  14. [OMICS AND BIG DATA, MAJOR ADVANCES TOWARDS PERSONALIZED MEDICINE OF THE FUTURE?].

    Science.gov (United States)

    Scheen, A J

    2015-01-01

    The increasing interest for personalized medicine evolves together with two major technological advances. First, the new-generation, rapid and less expensive, DNA sequencing method, combined with remarkable progresses in molecular biology leading to the post-genomic era (transcriptomics, proteomics, metabolomics). Second, the refinement of computing tools (IT), which allows the immediate analysis of a huge amount of data (especially, those resulting from the omics approaches) and, thus, creates a new universe for medical research, that of analyzed by computerized modelling. This article for scientific communication and popularization briefly describes the main advances in these two fields of interest. These technological progresses are combined with those occurring in communication, which makes possible the development of artificial intelligence. These major advances will most probably represent the grounds of the future personalized medicine.

  15. Multi-platform ’Omics Analysis of Human Ebola Virus Disease Pathogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Eisfeld, Amie J.; Halfmann, Peter J.; Wendler, Jason P.; Kyle, Jennifer E.; Burnum-Johnson, Kristin E.; Peralta, Zuleyma; Maemura, Tadashi; Walters, Kevin B.; Watanabe, Tokiko; Fukuyama, Satoshi; Yamashita, Makoto; Jacobs, Jon M.; Kim, Young-Mo; Casey, Cameron P.; Stratton, Kelly G.; Webb-Robertson, Bobbie-Jo M.; Gritsenko, Marina A.; Monroe, Matthew E.; Weitz, Karl K.; Shukla, Anil K.; Tian, Mingyuan; Neumann, Gabriele; Reed, Jennifer L.; van Bakel, Harm; Metz, Thomas O.; Smith, Richard D.; Waters, Katrina M.; N' jai, Alhaji; Sahr, Foday; Kawaoka, Yoshihiro

    2017-12-01

    The pathogenesis of human Ebola virus disease (EVD) is complex. EVD is characterized by high levels of virus replication and dissemination, dysregulated immune responses, extensive virus- and host-mediated tissue damage, and disordered coagulation. To clarify how host responses contribute to EVD pathophysiology, we performed multi-platform ’omics analysis of peripheral blood mononuclear cells and plasma from EVD patients. Our results indicate that EVD molecular signatures overlap with those of sepsis, imply that pancreatic enzymes contribute to tissue damage in fatal EVD, and suggest that Ebola virus infection may induce aberrant neutrophils whose activity could explain hallmarks of fatal EVD. Moreover, integrated biomarker prediction identified putative biomarkers from different data platforms that differentiated survivors and fatalities early after infection. This work reveals insight into EVD pathogenesis, suggests an effective approach for biomarker identification, and provides an important community resource for further analysis of human EVD severity.

  16. Stemcell Information: SKIP000806 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available change : every day No 5% Negative ... RIKEN BioResouce Center (RIKEN ... BRC) 理化学...研究所バイオリソースセンター RIKEN BioResouce Center (RIKEN ... BRC) 理化学研究所バイオリソースセンター Available RIKEN BioR...esouce Center (RIKEN ... BRC) 理化学研究所バイオリソースセンター http://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HPS0059&type=1 ...

  17. Omics approaches in fish quality and safety

    Directory of Open Access Journals (Sweden)

    Maria Lúcia Guerra Monteiro

    2017-05-01

    Full Text Available Omics is a new technology that uses genomics, proteomics, and metabolomics to investigate metabolites from foods. The global demand for fish has shown a progressive increase because it is a significant source of high quality protein, polyunsaturated fatty acids, especially omega-3, and essential minerals. However, there are barriers in the fishery production chain such as lack of standardization, knowledge, and technology transfer to industry. Moreover, fish effective monitoring is difficult due to restricted quality parameters and analytical methods determined by current Brazilian legislation. This review details the limiting chemical parameters and recent advances in analytical procedures for fish quality determination. To improve fish quality monitoring, total volatile basic nitrogen (TVB-N, trimethylamine (TMA, ammonia, pH, and biogenic amines values should be revised and established by fish category and/or type of fish product. On the other hand, protein carbonyl concentration, free fatty acids (FFAs, peroxide values (POV, and thiobarbituric acid reactive substances (TBARS should be included in the national legislation. Simultaneously, the official authorities should take into account effective, practical, and low cost analytical methodologies, which lead to faster results in order to facilitate and enhance the quality control of the products from the fish production chain, ensuring the consumer’s health. Moreover, analytical techniques for the identification of fish species must be introduced in the Brazilian legislation in order to avoid illegal substitutions and negative impacts to consumers.

  18. NuChart: an R package to study gene spatial neighbourhoods with multi-omics annotations.

    Directory of Open Access Journals (Sweden)

    Ivan Merelli

    Full Text Available Long-range chromosomal associations between genomic regions, and their repositioning in the 3D space of the nucleus, are now considered to be key contributors to the regulation of gene expression and important links have been highlighted with other genomic features involved in DNA rearrangements. Recent Chromosome Conformation Capture (3C measurements performed with high throughput sequencing (Hi-C and molecular dynamics studies show that there is a large correlation between colocalization and coregulation of genes, but these important researches are hampered by the lack of biologists-friendly analysis and visualisation software. Here, we describe NuChart, an R package that allows the user to annotate and statistically analyse a list of input genes with information relying on Hi-C data, integrating knowledge about genomic features that are involved in the chromosome spatial organization. NuChart works directly with sequenced reads to identify the related Hi-C fragments, with the aim of creating gene-centric neighbourhood graphs on which multi-omics features can be mapped. Predictions about CTCF binding sites, isochores and cryptic Recombination Signal Sequences are provided directly with the package for mapping, although other annotation data in bed format can be used (such as methylation profiles and histone patterns. Gene expression data can be automatically retrieved and processed from the Gene Expression Omnibus and ArrayExpress repositories to highlight the expression profile of genes in the identified neighbourhood. Moreover, statistical inferences about the graph structure and correlations between its topology and multi-omics features can be performed using Exponential-family Random Graph Models. The Hi-C fragment visualisation provided by NuChart allows the comparisons of cells in different conditions, thus providing the possibility of novel biomarkers identification. NuChart is compliant with the Bioconductor standard and it is freely

  19. Omics analysis of acetic acid tolerance in Saccharomyces cerevisiae.

    Science.gov (United States)

    Geng, Peng; Zhang, Liang; Shi, Gui Yang

    2017-05-01

    Acetic acid is an inhibitor in industrial processes such as wine making and bioethanol production from cellulosic hydrolysate. It causes energy depletion, inhibition of metabolic enzyme activity, growth arrest and ethanol productivity losses in Saccharomyces cerevisiae. Therefore, understanding the mechanisms of the yeast responses to acetic acid stress is essential for improving acetic acid tolerance and ethanol production. Although 329 genes associated with acetic acid tolerance have been identified in the Saccharomyces genome and included in the database ( http://www.yeastgenome.org/observable/resistance_to_acetic_acid/overview ), the cellular mechanistic responses to acetic acid remain unclear in this organism. Post-genomic approaches such as transcriptomics, proteomics, metabolomics and chemogenomics are being applied to yeast and are providing insight into the mechanisms and interactions of genes, proteins and other components that together determine complex quantitative phenotypic traits such as acetic acid tolerance. This review focuses on these omics approaches in the response to acetic acid in S. cerevisiae. Additionally, several novel strains with improved acetic acid tolerance have been engineered by modifying key genes, and the application of these strains and recently acquired knowledge to industrial processes is also discussed.

  20. Metabolic reconstruction of Setaria italica: a systems biology approach for integrating tissue-specific omics and pathway analysis of bioenergy grasses

    Directory of Open Access Journals (Sweden)

    Cristiana Gomes De Oliveira Dal'molin

    2016-08-01

    Full Text Available The urgent need for major gains in industrial crops productivity and in biofuel production from bioenergy grasses have reinforced attention on understanding C4 photosynthesis. Systems biology studies of C4 model plants may reveal important features of C4 metabolism. Here we chose foxtail millet (Setaria italica, as a C4 model plant and developed protocols to perform systems biology studies. As part of the systems approach, we have developed and used a genome-scale metabolic reconstruction in combination with the use of multi-omics technologies to gain more insights into the metabolism of S.italica. mRNA, protein and metabolite abundances, were measured in mature and immature stem/leaf phytomers and the multi-omics data were integrated into the metabolic reconstruction framework to capture key metabolic features in different developmental stages of the plant. RNA-Seq reads were mapped to the S. italica resulting for 83% coverage of the protein coding genes of S. italica. Besides revealing similarities and differences in central metabolism of mature and immature tissues, transcriptome analysis indicates significant gene expression of two malic enzyme isoforms (NADP- ME and NAD-ME. Although much greater expression levels of NADP-ME genes are observed and confirmed by the correspondent protein abundances in the samples, the expression of multiple genes combined to the significant abundance of metabolites that participates in C4 metabolism of NAD-ME and NADP-ME subtypes suggest that S. italica may use mixed decarboxylation modes of C4 photosynthetic pathways under different plant developmental stages. The overall analysis also indicates different levels of regulation in mature and immature tissues in carbon fixation, glycolysis, TCA cycle, amino acids, fatty acids, lignin and cellulose syntheses. Altogether, the multi-omics analysis reveals different biological entities and their interrelation and regulation over plant development. With this study

  1. Metabolic Reconstruction of Setaria italica: A Systems Biology Approach for Integrating Tissue-Specific Omics and Pathway Analysis of Bioenergy Grasses.

    Science.gov (United States)

    de Oliveira Dal'Molin, Cristiana G; Orellana, Camila; Gebbie, Leigh; Steen, Jennifer; Hodson, Mark P; Chrysanthopoulos, Panagiotis; Plan, Manuel R; McQualter, Richard; Palfreyman, Robin W; Nielsen, Lars K

    2016-01-01

    The urgent need for major gains in industrial crops productivity and in biofuel production from bioenergy grasses have reinforced attention on understanding C4 photosynthesis. Systems biology studies of C4 model plants may reveal important features of C4 metabolism. Here we chose foxtail millet (Setaria italica), as a C4 model plant and developed protocols to perform systems biology studies. As part of the systems approach, we have developed and used a genome-scale metabolic reconstruction in combination with the use of multi-omics technologies to gain more insights into the metabolism of S. italica. mRNA, protein, and metabolite abundances, were measured in mature and immature stem/leaf phytomers, and the multi-omics data were integrated into the metabolic reconstruction framework to capture key metabolic features in different developmental stages of the plant. RNA-Seq reads were mapped to the S. italica resulting for 83% coverage of the protein coding genes of S. italica. Besides revealing similarities and differences in central metabolism of mature and immature tissues, transcriptome analysis indicates significant gene expression of two malic enzyme isoforms (NADP- ME and NAD-ME). Although much greater expression levels of NADP-ME genes are observed and confirmed by the correspondent protein abundances in the samples, the expression of multiple genes combined to the significant abundance of metabolites that participates in C4 metabolism of NAD-ME and NADP-ME subtypes suggest that S. italica may use mixed decarboxylation modes of C4 photosynthetic pathways under different plant developmental stages. The overall analysis also indicates different levels of regulation in mature and immature tissues in carbon fixation, glycolysis, TCA cycle, amino acids, fatty acids, lignin, and cellulose syntheses. Altogether, the multi-omics analysis reveals different biological entities and their interrelation and regulation over plant development. With this study, we demonstrated

  2. Omics for Investigating Chitosan as an Antifungal and Gene Modulator

    Directory of Open Access Journals (Sweden)

    Federico Lopez-Moya

    2016-03-01

    Full Text Available Chitosan is a biopolymer with a wide range of applications. The use of chitosan in clinical medicine to control infections by fungal pathogens such as Candida spp. is one of its most promising applications in view of the reduced number of antifungals available. Chitosan increases intracellular oxidative stress, then permeabilizes the plasma membrane of sensitive filamentous fungus Neurospora crassa and yeast. Transcriptomics reveals plasma membrane homeostasis and oxidative metabolism genes as key players in the response of fungi to chitosan. A lipase and a monosaccharide transporter, both inner plasma membrane proteins, and a glutathione transferase are main chitosan targets in N. crassa. Biocontrol fungi such as Pochonia chlamydosporia have a low content of polyunsaturated free fatty acids in their plasma membranes and are resistant to chitosan. Genome sequencing of P. chlamydosporia reveals a wide gene machinery to degrade and assimilate chitosan. Chitosan increases P. chlamydosporia sporulation and enhances parasitism of plant parasitic nematodes by the fungus. Omics studies allow understanding the mode of action of chitosan and help its development as an antifungal and gene modulator.

  3. Signalling entropy: A novel network-theoretical framework for systems analysis and interpretation of functional omic data.

    Science.gov (United States)

    Teschendorff, Andrew E; Sollich, Peter; Kuehn, Reimer

    2014-06-01

    A key challenge in systems biology is the elucidation of the underlying principles, or fundamental laws, which determine the cellular phenotype. Understanding how these fundamental principles are altered in diseases like cancer is important for translating basic scientific knowledge into clinical advances. While significant progress is being made, with the identification of novel drug targets and treatments by means of systems biological methods, our fundamental systems level understanding of why certain treatments succeed and others fail is still lacking. We here advocate a novel methodological framework for systems analysis and interpretation of molecular omic data, which is based on statistical mechanical principles. Specifically, we propose the notion of cellular signalling entropy (or uncertainty), as a novel means of analysing and interpreting omic data, and more fundamentally, as a means of elucidating systems-level principles underlying basic biology and disease. We describe the power of signalling entropy to discriminate cells according to differentiation potential and cancer status. We further argue the case for an empirical cellular entropy-robustness correlation theorem and demonstrate its existence in cancer cell line drug sensitivity data. Specifically, we find that high signalling entropy correlates with drug resistance and further describe how entropy could be used to identify the achilles heels of cancer cells. In summary, signalling entropy is a deep and powerful concept, based on rigorous statistical mechanical principles, which, with improved data quality and coverage, will allow a much deeper understanding of the systems biological principles underlying normal and disease physiology. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. The medical science DMZ: a network design pattern for data-intensive medical science

    Energy Technology Data Exchange (ETDEWEB)

    Peisert, Sean [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Davis, CA (United States). Dept. of computer Science; Corporation for Education Network Initiatives in California (CENIC), Berkeley, CA (United States); Dart, Eli [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). ESnet; Barnett, William [Indiana Univ., Indianapolis, IN (United States). Indiana Clinical and Translational Sciences Inst., Regenstrief Inst.; Balas, Edward [Indiana Univ., Bloomington, IN (United States). Global Research Network Operations Center; Cuff, James [Harvard Univ., Cambridge, MA (United States). Research Computing; Grossman, Robert L. [Univ. of Chicago, IL (United States). Center for Data Intensive Science; Berman, Ari [BioTeam, Middleton, MA (United States); Shankar, Anurag [Indiana Univ., Bloomington, IN (United States). Pervasive Technology Inst.; Tierney, Brian [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). ESnet

    2017-10-06

    We describe a detailed solution for maintaining high-capacity, data-intensive network flows (eg, 10, 40, 100 Gbps+) in a scientific, medical context while still adhering to security and privacy laws and regulations.High-end networking, packet-filter firewalls, network intrusion-detection systems.We describe a "Medical Science DMZ" concept as an option for secure, high-volume transport of large, sensitive datasets between research institutions over national research networks, and give 3 detailed descriptions of implemented Medical Science DMZs.The exponentially increasing amounts of "omics" data, high-quality imaging, and other rapidly growing clinical datasets have resulted in the rise of biomedical research "Big Data." The storage, analysis, and network resources required to process these data and integrate them into patient diagnoses and treatments have grown to scales that strain the capabilities of academic health centers. Some data are not generated locally and cannot be sustained locally, and shared data repositories such as those provided by the National Library of Medicine, the National Cancer Institute, and international partners such as the European Bioinformatics Institute are rapidly growing. The ability to store and compute using these data must therefore be addressed by a combination of local, national, and industry resources that exchange large datasets. Maintaining data-intensive flows that comply with the Health Insurance Portability and Accountability Act (HIPAA) and other regulations presents a new challenge for biomedical research. We describe a strategy that marries performance and security by borrowing from and redefining the concept of a Science DMZ, a framework that is used in physical sciences and engineering research to manage high-capacity data flows.By implementing a Medical Science DMZ architecture, biomedical researchers can leverage the scale provided by high-performance computer and cloud storage facilities and national high

  5. An approach for optimally extending mathematical models of signaling networks using omics data.

    Science.gov (United States)

    Bianconi, Fortunato; Patiti, Federico; Baldelli, Elisa; Crino, Lucio; Valigi, Paolo

    2015-01-01

    Mathematical modeling is a key process in Systems Biology and the use of computational tools such as Cytoscape for omics data processing, need to be integrated in the modeling activity. In this paper we propose a new methodology for modeling signaling networks by combining ordinary differential equation models and a gene recommender system, GeneMANIA. We started from existing models, that are stored in the BioModels database, and we generated a query to use as input for the GeneMANIA algorithm. The output of the recommender system was then led back to the kinetic reactions that were finally added to the starting model. We applied the proposed methodology to EGFR-IGF1R signal transduction network, which plays an important role in translational oncology and cancer therapy of non small cell lung cancer.

  6. Scientific articles of the RBRC/CCAST Symposium on Spin Physics Lattice QCD and RHIC Physics

    International Nuclear Information System (INIS)

    2003-01-01

    This volume comprises scientific articles of the symposium on spin physics, lattice QCD and RHIC physics organized by RIKEN BNL research center (RBRC) and China center of advanced science and technology (CCAST). The talks were discussing the spin structure of nucleons and other problems of RHIC physics

  7. Toward Omics-Based, Systems Biomedicine, and Path and Drug Discovery Methodologies for Depression-Inflammation Research.

    Science.gov (United States)

    Maes, Michael; Nowak, Gabriel; Caso, Javier R; Leza, Juan Carlos; Song, Cai; Kubera, Marta; Klein, Hans; Galecki, Piotr; Noto, Cristiano; Glaab, Enrico; Balling, Rudi; Berk, Michael

    2016-07-01

    Meta-analyses confirm that depression is accompanied by signs of inflammation including increased levels of acute phase proteins, e.g., C-reactive protein, and pro-inflammatory cytokines, e.g., interleukin-6. Supporting the translational significance of this, a meta-analysis showed that anti-inflammatory drugs may have antidepressant effects. Here, we argue that inflammation and depression research needs to get onto a new track. Firstly, the choice of inflammatory biomarkers in depression research was often too selective and did not consider the broader pathways. Secondly, although mild inflammatory responses are present in depression, other immune-related pathways cannot be disregarded as new drug targets, e.g., activation of cell-mediated immunity, oxidative and nitrosative stress (O&NS) pathways, autoimmune responses, bacterial translocation, and activation of the toll-like receptor and neuroprogressive pathways. Thirdly, anti-inflammatory treatments are sometimes used without full understanding of their effects on the broader pathways underpinning depression. Since many of the activated immune-inflammatory pathways in depression actually confer protection against an overzealous inflammatory response, targeting these pathways may result in unpredictable and unwanted results. Furthermore, this paper discusses the required improvements in research strategy, i.e., path and drug discovery processes, omics-based techniques, and systems biomedicine methodologies. Firstly, novel methods should be employed to examine the intracellular networks that control and modulate the immune, O&NS and neuroprogressive pathways using omics-based assays, including genomics, transcriptomics, proteomics, metabolomics, epigenomics, immunoproteomics and metagenomics. Secondly, systems biomedicine analyses are essential to unravel the complex interactions between these cellular networks, pathways, and the multifactorial trigger factors and to delineate new drug targets in the cellular

  8. Plant phenotype - Arabidopsis Phenome Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available of organs, tissues, development stages. The vocabulary is defined in Plant Ontology(PO). Qualities: Characte...ristics, attributes of entities. The vocabulary is defined in Phenotype Ontology(PATO). Data file File name:...w/riken_piam_phenome#en Data acquisition method Plant Ontology, Phenotype Ontology Data analysis method - Nu

  9. Proceedings of the cross-over symposium 'new approaches for studies on environmental radioactivity'

    International Nuclear Information System (INIS)

    Matsumoto, Shiro; Uchida, Shigeo; Yamazawa, Hiromi; Amano, Hikaru

    1999-03-01

    This conference was organized by the Promotion Committee on Nuclear Cross-Over Research and the Specialist Committee on Assessment and Reduction of Radiation Risks, and co-organized by Microbial Toxicology Lab., RIKEN and Environmental Chemistry Lab., JAERI. In 1991, a project on transfer models and parameters of radionuclides in terrestrial environment was started in the Specialist Committee on Assessment and Reduction of Radiation Risks. This project was finished successfully to have active cooperation of different organizations which were Japan Atomic Energy Research Institute (JAERI), Meteorological Research Institute (MRI), National Institute of Radiological Sciences (NIRS), the Institute of Physical and Chemical Research (RIKEN) and Power Reactor and Nuclear Fuel Development Corporation (PNC). Subsequently, we started a new project named 'Development of dynamic models of transfer of radionuclides in the terrestrial environment' with adding a new member, Institute for Environmental Sciences (IES) from 1996. The results we obtained so far were presented in this conference. The 20 of the presented papers are indexed individually. (J.P.N.)

  10. Proceedings of the cross-over symposium `new approaches for studies on environmental radioactivity`

    Energy Technology Data Exchange (ETDEWEB)

    Matsumoto, Shiro [Saitama Univ., Urawa (Japan); Uchida, Shigeo; Yamazawa, Hiromi; Amano, Hikaru [eds.

    1999-03-01

    This conference was organized by the Promotion Committee on Nuclear Cross-Over Research and the Specialist Committee on Assessment and Reduction of Radiation Risks, and co-organized by Microbial Toxicology Lab., RIKEN and Environmental Chemistry Lab., JAERI. In 1991, a project on transfer models and parameters of radionuclides in terrestrial environment was started in the Specialist Committee on Assessment and Reduction of Radiation Risks. This project was finished successfully to have active cooperation of different organizations which were Japan Atomic Energy Research Institute (JAERI), Meteorological Research Institute (MRI), National Institute of Radiological Sciences (NIRS), the Institute of Physical and Chemical Research (RIKEN) and Power Reactor and Nuclear Fuel Development Corporation (PNC). Subsequently, we started a new project named `Development of dynamic models of transfer of radionuclides in the terrestrial environment` with adding a new member, Institute for Environmental Sciences (IES) from 1996. The results we obtained so far were presented in this conference. The 20 of the presented papers are indexed individually. (J.P.N.)

  11. Study of cnidarian-algal symbiosis in the "omics" age.

    Science.gov (United States)

    Meyer, Eli; Weis, Virginia M

    2012-08-01

    The symbiotic associations between cnidarians and dinoflagellate algae (Symbiodinium) support productive and diverse ecosystems in coral reefs. Many aspects of this association, including the mechanistic basis of host-symbiont recognition and metabolic interaction, remain poorly understood. The first completed genome sequence for a symbiotic anthozoan is now available (the coral Acropora digitifera), and extensive expressed sequence tag resources are available for a variety of other symbiotic corals and anemones. These resources make it possible to profile gene expression, protein abundance, and protein localization associated with the symbiotic state. Here we review the history of "omics" studies of cnidarian-algal symbiosis and the current availability of sequence resources for corals and anemones, identifying genes putatively involved in symbiosis across 10 anthozoan species. The public availability of candidate symbiosis-associated genes leaves the field of cnidarian-algal symbiosis poised for in-depth comparative studies of sequence diversity and gene expression and for targeted functional studies of genes associated with symbiosis. Reviewing the progress to date suggests directions for future investigations of cnidarian-algal symbiosis that include (i) sequencing of Symbiodinium, (ii) proteomic analysis of the symbiosome membrane complex, (iii) glycomic analysis of Symbiodinium cell surfaces, and (iv) expression profiling of the gastrodermal cells hosting Symbiodinium.

  12. The Multitracer technique: manufacturing and application to bio-trace elemental research

    International Nuclear Information System (INIS)

    Enomoto, Shuichi; Hirunuma, Rieko

    2002-01-01

    A versatile radioactive multitracer technique has been developed at RIKEN Accelerator Research Facility about 11 years before. It enables efficient and simultaneous tracing of a number of elements under identical experimental conditions. Since 1991, the multitracer technique has been applied for an investigation of a behavior of various elements in chemistry, biochemistry, pharmaceutical sciences, medical sciences, nutritional sciences, agricultural sciences, and environmental sciences. Now, the multitracer has been used in more than 50 laboratories in the world. Its principle and features are presented with examples of recent application. (author)

  13. Somatic Embryogenesis in Coffee: The Evolution of Biotechnology and the Integration of Omics Technologies Offer Great Opportunities.

    Science.gov (United States)

    Campos, Nádia A; Panis, Bart; Carpentier, Sebastien C

    2017-01-01

    One of the most important crops cultivated around the world is coffee. There are two main cultivated species, Coffea arabica and C. canephora. Both species are difficult to improve through conventional breeding, taking at least 20 years to produce a new cultivar. Biotechnological tools such as genetic transformation, micropropagation and somatic embryogenesis (SE) have been extensively studied in order to provide practical results for coffee improvement. While genetic transformation got many attention in the past and is booming with the CRISPR technology, micropropagation and SE are still the major bottle neck and urgently need more attention. The methodologies to induce SE and the further development of the embryos are genotype-dependent, what leads to an almost empirical development of specific protocols for each cultivar or clone. This is a serious limitation and excludes a general comprehensive understanding of the process as a whole. The aim of this review is to provide an overview of which achievements and molecular insights have been gained in (coffee) somatic embryogenesis and encourage researchers to invest further in the in vitro technology and combine it with the latest omics techniques (genomics, transcriptomics, proteomics, metabolomics, and phenomics). We conclude that the evolution of biotechnology and the integration of omics technologies offer great opportunities to (i) optimize the production process of SE and the subsequent conversion into rooted plantlets and (ii) to screen for possible somaclonal variation. However, currently the usage of the latest biotechnology did not pass the stage beyond proof of potential and needs to further improve.

  14. HARD PARTON PHYSICS IN HIGH ENERGY NUCLEAR COLLISIONS. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP, VOLUME 17

    Energy Technology Data Exchange (ETDEWEB)

    CARROLL,J.

    1999-09-10

    The RIKEN-BNL center workshop on ''Hard parton physics in high energy nuclear collisions'' was held at BNL from March 1st-5th! 1999. The focus of the workshop was on hard probes of nucleus-nucleus collisions that will be measured at RHIC with the PHENIX and STAR detectors. There were about 45 speakers and over 70 registered participants at the workshop, with roughly a quarter of the speakers from overseas. About 60% of the talks were theory talks. A nice overview of theory for RHIC was provided by George Sterman. The theoretical talks were on a wide range of topics in QCD which can be classified under the following: (a) energy loss and the Landau-Pomeranchuk-Migdal effect; (b) minijet production and equilibration; (c) small x physics and initial conditions; (d) nuclear parton distributions and shadowing; (e) spin physics; (f) photon, di-lepton, and charm production; and (g) hadronization, and simulations of high pt physics in event generators. Several of the experimental talks discussed the capabilities of the PHENIX and STAR detectors at RHIC in measuring high pt particles in heavy ion collisions. In general, these talks were included in the relevant theory sessions. A session was set aside to discuss the spin program at RHIC with polarized proton beams. In addition, there were speakers from 08, HERA, the fixed target experiments at Fermilab, and the CERN fixed target Pb+Pb program, who provided additional perspective on a range of issues of relevance to RHIC; from jets at the Tevatron, to saturation of parton distributions at HERA, and recent puzzling data on direct photon production in fixed target experiments, among others.

  15. A multi-omics based ecological analysis of coastal marine sediments from Gladstone, in Australia's Central Queensland, and Heron Island, a nearby fringing platform reef.

    Science.gov (United States)

    Beale, D J; Crosswell, J; Karpe, A V; Ahmed, W; Williams, M; Morrison, P D; Metcalfe, S; Staley, C; Sadowsky, M J; Palombo, E A; Steven, A D L

    2017-12-31

    The impact of anthropogenic factors arising from point and non-point pollution sources at a multi commodity marine port and its surrounding ecosystems were studied using sediment samples collected from a number of onshore (Gladstone Harbour and Facing Island) and offshore (Heron Island and Fitzroy Reefs) sites in Australia's Central Queensland. Sediment samples were analyzed for trace metals, organic carbon, polycyclic aromatic hydrocarbons (PAH), emerging chemicals of concern (ECC) and sterols. Similarly, the biological and biochemical interaction between the reef and its environment was analyzed by the multi-omic tools of next-generation sequencing characterization of the bacterial community and microbial community metabolic profiling. Overall, the trace elements were observed at the lower end of the Australian environmental guideline values at the offshore sites, while higher values were observed for the onshore locations Nickel and copper were observed above the high trigger value threshold at the onshore sites. The levels of PAH were below limits of detection across all sites. However, some of the ECC and sterols were observed at higher concentrations at both onshore and offshore locations, notably, the cholesterol family sterols and 17α-ethynylestradiol. Multi-omic analyses also indicated possible thermal and photo irradiation stressors on the bacterial communities at all the tested sites. The observed populations of γ-proteobacteria were found in combination with an increased pool of fatty acids that indicate fatty acid synthesis and utilisation of the intermediates of the shikimate pathways. This study demonstrates the value of applying a multi-omics approach for ecological assessments, in which a more detailed assessment of physical and chemical contaminants and their impact on the community bacterial biome is obtained. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  16. Exploring the post-genomic world: differing explanatory and manipulatory functions of post-genomic sciences.

    Science.gov (United States)

    Holmes, Christina; Carlson, Siobhan M; McDonald, Fiona; Jones, Mavis; Graham, Janice

    2016-01-02

    Richard Lewontin proposed that the ability of a scientific field to create a narrative for public understanding garners it social relevance. This article applies Lewontin's conceptual framework of the functions of science (manipulatory and explanatory) to compare and explain the current differences in perceived societal relevance of genetics/genomics and proteomics. We provide three examples to illustrate the social relevance and strong cultural narrative of genetics/genomics for which no counterpart exists for proteomics. We argue that the major difference between genetics/genomics and proteomics is that genomics has a strong explanatory function, due to the strong cultural narrative of heredity. Based on qualitative interviews and observations of proteomics conferences, we suggest that the nature of proteins, lack of public understanding, and theoretical complexity exacerbates this difference for proteomics. Lewontin's framework suggests that social scientists may find that omics sciences affect social relations in different ways than past analyses of genetics.

  17. Dissecting Candida albicans Infection from the Perspective of C. albicans Virulence and Omics Approaches on Host–Pathogen Interaction: A Review

    Directory of Open Access Journals (Sweden)

    Voon Kin Chin

    2016-10-01

    Full Text Available Candida bloodstream infections remain the most frequent life-threatening fungal disease, with Candida albicans accounting for 70% to 80% of the Candida isolates recovered from infected patients. In nature, Candida species are part of the normal commensal flora in mammalian hosts. However, they can transform into pathogens once the host immune system is weakened or breached. More recently, mortality attributed to Candida infections has continued to increase due to both inherent and acquired drug resistance in Candida, the inefficacy of the available antifungal drugs, tedious diagnostic procedures, and a rising number of immunocompromised patients. Adoption of animal models, viz. minihosts, mice, and zebrafish, has brought us closer to unraveling the pathogenesis and complexity of Candida infection in human hosts, leading towards the discovery of biomarkers and identification of potential therapeutic agents. In addition, the advancement of omics technologies offers a holistic view of the Candida-host interaction in a non-targeted and non-biased manner. Hence, in this review, we seek to summarize past and present milestone findings on C. albicans virulence, adoption of animal models in the study of C. albicans infection, and the application of omics technologies in the study of Candida–host interaction. A profound understanding of the interaction between host defense and pathogenesis is imperative for better design of novel immunotherapeutic strategies in future.

  18. The use of 'Omics technology to rationally improve industrial mammalian cell line performance.

    Science.gov (United States)

    Lewis, Amanda M; Abu-Absi, Nicholas R; Borys, Michael C; Li, Zheng Jian

    2016-01-01

    Biologics represent an increasingly important class of therapeutics, with 7 of the 10 top selling drugs from 2013 being in this class. Furthermore, health authority approval of biologics in the immuno-oncology space is expected to transform treatment of patients with debilitating and deadly diseases. The growing importance of biologics in the healthcare field has also resulted in the recent approvals of several biosimilars. These recent developments, combined with pressure to provide treatments at lower costs to payers, are resulting in increasing need for the industry to quickly and efficiently develop high yielding, robust processes for the manufacture of biologics with the ability to control quality attributes within narrow distributions. Achieving this level of manufacturing efficiency and the ability to design processes capable of regulating growth, death and other cellular pathways through manipulation of media, feeding strategies, and other process parameters will undoubtedly be facilitated through systems biology tools generated in academic and public research communities. Here we discuss the intersection of systems biology, 'Omics technologies, and mammalian bioprocess sciences. Specifically, we address how these methods in conjunction with traditional monitoring techniques represent a unique opportunity to better characterize and understand host cell culture state, shift from an empirical to rational approach to process development and optimization of bioreactor cultivation processes. We summarize the following six key areas: (i) research applied to parental, non-recombinant cell lines; (ii) systems level datasets generated with recombinant cell lines; (iii) datasets linking phenotypic traits to relevant biomarkers; (iv) data depositories and bioinformatics tools; (v) in silico model development, and (vi) examples where these approaches have been used to rationally improve cellular processes. We critically assess relevant and state of the art research

  19. Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling.

    Science.gov (United States)

    Vijayakumar, Supreeta; Conway, Max; Lió, Pietro; Angione, Claudio

    2017-05-30

    Metabolic modelling has entered a mature phase with dozens of methods and software implementations available to the practitioner and the theoretician. It is not easy for a modeller to be able to see the wood (or the forest) for the trees. Driven by this analogy, we here present a 'forest' of principal methods used for constraint-based modelling in systems biology. This provides a tree-based view of methods available to prospective modellers, also available in interactive version at http://modellingmetabolism.net, where it will be kept updated with new methods after the publication of the present manuscript. Our updated classification of existing methods and tools highlights the most promising in the different branches, with the aim to develop a vision of how existing methods could hybridize and become more complex. We then provide the first hands-on tutorial for multi-objective optimization of metabolic models in R. We finally discuss the implementation of multi-view machine learning approaches in poly-omic integration. Throughout this work, we demonstrate the optimization of trade-offs between multiple metabolic objectives, with a focus on omic data integration through machine learning. We anticipate that the combination of a survey, a perspective on multi-view machine learning and a step-by-step R tutorial should be of interest for both the beginner and the advanced user. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  20. Effects of radiation on model plant rice - OMICS: Recent progress and future prospects

    International Nuclear Information System (INIS)

    Rakwal, Randeep; Shibato, Junko; Agrawal, Ganesh Kumar; Imanaka, Tetsuji; Fukutani, Satoshi; Tamogami, Shigeru; Endo, Satoru; Sahoo, Sarat Kumar; Kimura, Shinzo

    2011-01-01

    This is the age of functional genomics, where genomes to high-throughput technologies and to the phenotype are making inroads into various biological questions and problems. In this report, I along with my co-workers will present an outline into the omics approaches, focusing on the global gene expression profiling (DNA microarray technique), plants and the environment, and culminating in the use of genomics to analyze the effects of radiation on plant life. For this, rice (Oryza sativa L.) geonome model and monocot cereal crop plant will be used as an example. It is our hope that use of both model and non-model plants in conjunction with high-throughput transcriptomics approaches will lead the way for unraveling radiation responses in plants, setting the stage for further research on this important aspect of our environment with direct and indirect impact on human life and civilization. (author)

  1. Determining Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: PART A-Radiomics

    Czech Academy of Sciences Publication Activity Database

    Falk, Martin; Hausmann, M.; Lukášová, Emilie; Biswas, A.; Hildenbrand, G.; Davídková, Marie; Krasavin, E.; Kleibl, Z.; Falková, Iva; Ježková, L.

    2014-01-01

    Roč. 24, č. 3 (2014), s. 205-223 ISSN 1045-4403 R&D Projects: GA ČR(CZ) GBP302/12/G157; GA ČR(CZ) GAP302/10/1022; GA MŠk(CZ) LD12039; GA MŠk(CZ) LD12008; GA MŠk(CZ) EE2.3.30.0030 Institutional support: RVO:68081707 ; RVO:61389005 Keywords : Omics * ionizing radiation * low-dose dilemma Subject RIV: BO - Biophysics; JF - Nuclear Energetics (UJF-V) Impact factor: 1.571, year: 2014

  2. Iron-Deficiency Anemia

    Medline Plus

    Full Text Available ... The Science Science Home Blood Disorders and Blood Safety Sleep Science and Sleep Disorders Lung Diseases Heart ... Donor Studies (REDS) program Blood Disorders and Blood Safety Trans-Omics for Precision Medicine (TOPMed) Program Non- ...

  3. Development of the multitracer technology for a simultaneous multi-elemental analysis and its evolution in RI-beam factory project

    International Nuclear Information System (INIS)

    Enomoto, Shuichi

    2003-01-01

    This review describes the method to produce the multitracer, its biobehavior, its application for environmental sciences, Nuclear Energy Fundamentals Crossover Research (for upgrading multitracer production technology, and development of the automatic chemical separation units and of the simultaneous imaging apparatus for multi gamma-ray nuclides), and Inst. of Physical and Chemical Research (RIKEN) RI-beam factory project. The multitracer technology is an efficient (i.e., many information's are available through one experimentation) tracer technique for studying the physical, chemical and biological behavior of elements with use of their multiple radioisotopes produced by accelerators like RIKEN ring cyclotron and of computer/semiconductor detector for their individual gamma-ray spectrometry. The multitracer elements are produced in their carrier-free forms by irradiation of the target element with the heavy particle (up to Ta, in RIKEN cyclotron) and by resultant nuclear fragmentation of the target. The multitracer through nuclear fragmentation and/or fission with an automated separation apparatus will be sophisticatedly supplied in future. GREI (gamma-ray emission imaging) is under investigation. The RI-beam factory project aims to irradiate/accelerate the radioisotope, which is expected to give novel knowledge's in biology like metabolic physiology. (N.I.)

  4. Proteomics in the fruit tree science arena: new insights into fruit defense, development, and ripening.

    Science.gov (United States)

    Molassiotis, Athanassios; Tanou, Georgia; Filippou, Panagiota; Fotopoulos, Vasileios

    2013-06-01

    Fruit tree crops are agricultural commodities of high economic importance, while fruits also represent one of the most vital components of the human diet. Therefore, a great effort has been made to understand the molecular mechanisms covering fundamental biological processes in fruit tree physiology and fruit biology. Thanks to the development of cutting-edge "omics" technologies such as proteomic analysis, scientists now have powerful tools to support traditional fruit tree research. Such proteomic analyses are establishing high-density 2DE reference maps and peptide mass fingerprint databases that can lead fruit science into a new postgenomic research era. Here, an overview of the application of proteomics in key aspects of fruit tree physiology as well as in fruit biology, including defense responses to abiotic and biotic stress factors, is presented. A panoramic view of ripening-related proteins is also discussed, as an example of proteomic application in fruit science.

  5. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP, HADRON STRUCTURE FROM LATTICE QCD, MARCH 18 - 22, 2002, BROOKHAVEN NATIONAL LABORATORY.

    Energy Technology Data Exchange (ETDEWEB)

    BLUM, T.; BOER, D.; CREUTZ, M.; OHTA, S.; ORGINOS, K.

    2002-03-18

    The RIKEN BNL Research Center workshop on ''Hadron Structure from Lattice QCD'' was held at BNL during March 11-15, 2002. Hadron structure has been the subject of many theoretical and experimental investigations, with significant success in understanding the building blocks of matter. The nonperturbative nature of QCD, however, has always been an obstacle to deepening our understanding of hadronic physics. Lattice QCD provides the tool to overcome these difficulties and hence a link can be established between the fundamental theory of QCD and hadron phenomenology. Due to the steady progress in improving lattice calculations over the years, comparison with experimentally measured hadronic quantities has become important. In this respect the workshop was especially timely. By providing an opportunity for experts from the lattice and hadron structure communities to present their latest results, the workshop enhanced the exchange of knowledge and ideas. With a total of 32 registered participants and 26 talks, the interest of a growing community is clearly exemplified. At the workshop Schierholz and Negele presented the current status of lattice computations of hadron structure. Substantial progress has been made during recent years now that the quenched results are well under control and the first dynamical results have appeared. In both the dynamical and the quenched simulations the lattice results, extrapolated to lighter quark masses, seem to disagree with experiment. Melnitchouk presented a possible explanation (chiral logs) for this disagreement. It became clear from these discussions that lattice computations at significantly lighter quark masses need to be performed.

  6. The medical science DMZ: a network design pattern for data-intensive medical science.

    Science.gov (United States)

    Peisert, Sean; Dart, Eli; Barnett, William; Balas, Edward; Cuff, James; Grossman, Robert L; Berman, Ari; Shankar, Anurag; Tierney, Brian

    2017-10-06

    We describe a detailed solution for maintaining high-capacity, data-intensive network flows (eg, 10, 40, 100 Gbps+) in a scientific, medical context while still adhering to security and privacy laws and regulations. High-end networking, packet-filter firewalls, network intrusion-detection systems. We describe a "Medical Science DMZ" concept as an option for secure, high-volume transport of large, sensitive datasets between research institutions over national research networks, and give 3 detailed descriptions of implemented Medical Science DMZs. The exponentially increasing amounts of "omics" data, high-quality imaging, and other rapidly growing clinical datasets have resulted in the rise of biomedical research "Big Data." The storage, analysis, and network resources required to process these data and integrate them into patient diagnoses and treatments have grown to scales that strain the capabilities of academic health centers. Some data are not generated locally and cannot be sustained locally, and shared data repositories such as those provided by the National Library of Medicine, the National Cancer Institute, and international partners such as the European Bioinformatics Institute are rapidly growing. The ability to store and compute using these data must therefore be addressed by a combination of local, national, and industry resources that exchange large datasets. Maintaining data-intensive flows that comply with the Health Insurance Portability and Accountability Act (HIPAA) and other regulations presents a new challenge for biomedical research. We describe a strategy that marries performance and security by borrowing from and redefining the concept of a Science DMZ, a framework that is used in physical sciences and engineering research to manage high-capacity data flows. By implementing a Medical Science DMZ architecture, biomedical researchers can leverage the scale provided by high-performance computer and cloud storage facilities and national high

  7. Investigation of Aspergillus fumigatus biofilm formation by various omics approaches

    Directory of Open Access Journals (Sweden)

    Laetitia eMuszkieta

    2013-02-01

    Full Text Available In the lung, Aspergillus fumigatus usually forms a dense colony of filaments embedded in a polymeric extracellular matrix called biofilm (BF. This extracellular matrix embeds and glues hyphae together and protects the fungus from an outside hostile environment. This extracellular matrix is absent in fungal colonies grown under classical liquid shake conditions (PL which were historically used to understand A. fumigatus pathobiology. Recent works have shown that the fungus in this aerial grown biofilm-like state exhibits reduced susceptibility to antifungal drugs and undergoes major metabolic changes that are thought to be associated to virulence. These differences in pathological and physiological characteristics between biofilm and liquid shake conditions suggest that the PL condition is a poor in vitro disease model. In the laboratory, A. fumigatus mycelium embedded by the extracellular matrix can be produced in vitro in aerial condition using an agar-based medium. To provide a global and accurate understanding of A. fumigatus in vitro biofilm growth, we utilized microarray, RNA-sequencing and proteomic analysis to compare the global gene and protein expression profiles of A. fumigatus grown under BF and PL conditions. In this review, we will present the different signatures obtained with these three omics methods. We will discuss the advantages and limitations of each method and their complementarity.

  8. Stemcell Information: SKIP000138 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 代 Riken Center for Developmental Biology (Riken CDB) 理研発生再生科学総合研究センター (理研CDB) Riken Center for Developmental... Biology (Riken CDB) 理研発生再生科学総合研究センター (理研CDB) Masayo Takahashi 高橋 政代 Available Ri

  9. Knowledge Translation: Moving Proteomics Science to Innovation in Society.

    Science.gov (United States)

    Holmes, Christina; McDonald, Fiona; Jones, Mavis; Graham, Janice

    2016-06-01

    Proteomics is one of the pivotal next-generation biotechnologies in the current "postgenomics" era. Little is known about the ways in which innovative proteomics science is navigating the complex socio-political space between laboratory and society. It cannot be assumed that the trajectory between proteomics laboratory and society is linear and unidirectional. Concerned about public accountability and hopes for knowledge-based innovations, funding agencies and citizens increasingly expect that emerging science and technologies, such as proteomics, are effectively translated and disseminated as innovation in society. Here, we describe translation strategies promoted in the knowledge translation (KT) and science communication literatures and examine the use of these strategies within the field of proteomics. Drawing on data generated from qualitative interviews with proteomics scientists and ethnographic observation of international proteomics conferences over a 5-year period, we found that proteomics science incorporates a variety of KT strategies to reach knowledge users outside the field. To attain the full benefit of KT, however, proteomics scientists must challenge their own normative assumptions and approaches to innovation dissemination-beyond the current paradigm relying primarily on publication for one's scientific peers within one's field-and embrace the value of broader (interdisciplinary) KT strategies in promoting the uptake of their research. Notably, the Human Proteome Organization (HUPO) is paying increasing attention to a broader range of KT strategies, including targeted dissemination, integrated KT, and public outreach. We suggest that increasing the variety of KT strategies employed by proteomics scientists is timely and would serve well the omics system sciences community.

  10. Multilayered Genetic and Omics Dissection of Mitochondrial Activity in a Mouse Reference Population

    Science.gov (United States)

    Wu, Yibo; Williams, Evan G.; Dubuis, Sébastien; Mottis, Adrienne; Jovaisaite, Virginija; Houten, Sander M.; Argmann, Carmen A.; Faridi, Pouya; Wolski, Witold; Kutalik, Zoltán; Zamboni, Nicola; Auwerx, Johan; Aebersold, Ruedi

    2014-01-01

    SUMMARY The manner by which genotype and environment affect complex phenotypes is one of the fundamental questions in biology. In this study, we quantified the transcriptome—a subset of the metabolome—and, using targeted proteomics, quantified a subset of the liver proteome from 40 strains of the BXD mouse genetic reference population on two diverse diets. We discovered dozens of transcript, protein, and metabolite QTLs, several of which linked to metabolic phenotypes. Most prominently, Dhtkd1 was identified as a primary regulator of 2-aminoadipate, explaining variance in fasted glucose and diabetes status in both mice and humans. These integrated molecular profiles also allowed further characterization of complex pathways, particularly the mitochondrial unfolded protein response (UPRmt). UPRmt shows strikingly variant responses at the transcript and protein level that are remarkably conserved among C. elegans, mice, and humans. Overall, these examples demonstrate the value of an integrated multilayered omics approach to characterize complex metabolic phenotypes. PMID:25215496

  11. An OMIC approach to elaborate the antibacterial mechanisms of different alkaloids.

    Science.gov (United States)

    Avci, Fatma Gizem; Sayar, Nihat Alpagu; Sariyar Akbulut, Berna

    2018-05-01

    Plant-derived substances have regained interest in the fight against antibiotic resistance owing to their distinct antimicrobial mechanisms and multi-target properties. With the recent advances in instrumentation and analysis techniques, OMIC approaches are extensively used for target identification and elucidation of the mechanism of phytochemicals in drug discovery. In the current study, RNA sequencing based transcriptional profiling together with global differential protein expression analysis was used to comparatively elaborate the activities and the effects of the plant alkaloids boldine, bulbocapnine, and roemerine along with the well-known antimicrobial alkaloid berberine in Bacillus subtilis cells. The transcriptomic findings were validated by qPCR. Images from scanning electron microscope were obtained to visualize the effects on the whole-cells. The results showed that among the three selected alkaloids, only roemerine possessed antibacterial activity. Unlike berberine, which is susceptible to efflux through multidrug resistance pumps, roemerine accumulated in the cells. This in turn resulted in oxidative stress and building up of reactive oxygen species, which eventually deregulated various pathways such as iron uptake. Treatment with boldine or bulbocapnine slightly affected various metabolic pathways but has not changed the growth patterns at all. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Single Cell Genomics in Marine Omics

    KAUST Repository

    Kodzius, Rimantas; Gojobori, Takashi

    2014-01-01

    Kingdom of Saudi Arabia invests heavily to both in infrastructure and science. King Abdullah University of Science and Technology (KAUST) is a modern and international university close to the Red Sea, with the focus on water, food, energy, and the environment.

  13. Single Cell Genomics in Marine Omics

    KAUST Repository

    Kodzius, Rimantas

    2014-09-10

    Kingdom of Saudi Arabia invests heavily to both in infrastructure and science. King Abdullah University of Science and Technology (KAUST) is a modern and international university close to the Red Sea, with the focus on water, food, energy, and the environment.

  14. Reference: 385 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 385 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u4ria224u16690816i Dharmasiri...y Science (New York, N.Y.) Bennett M J|Dharmasiri N|Dharmasiri S|Estelle M|Kowalchyk M|Marchant A|Mills S|Mockaitis K|Sandberg G|Singh S K|Swarup R

  15. The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown.

    Directory of Open Access Journals (Sweden)

    Shingo Miyauchi

    Full Text Available Innovative green technologies are of importance for converting plant wastes into renewable sources for materials, chemicals and energy. However, recycling agricultural and forestry wastes is a challenge. A solution may be found in the forest. Saprotrophic white-rot fungi are able to convert dead plants into consumable carbon sources. Specialized fungal enzymes can be utilized for breaking down hard plant biopolymers. Thus, understanding the enzymatic machineries of such fungi gives us hints for the efficient decomposition of plant materials. Using the saprotrophic white-rot fungus Pycnoporus coccineus as a fungal model, we examined the dynamics of transcriptomic and secretomic responses to different types of lignocellulosic substrates at two time points. Our integrative omics pipeline (SHIN+GO enabled us to compress layers of biological information into simple heatmaps, allowing for visual inspection of the data. We identified co-regulated genes with corresponding co-secreted enzymes, and the biological roles were extrapolated with the enriched Carbohydrate-Active Enzyme (CAZymes and functional annotations. We observed the fungal early responses for the degradation of lignocellulosic substrates including; 1 simultaneous expression of CAZy genes and secretion of the enzymes acting on diverse glycosidic bonds in cellulose, hemicelluloses and their side chains or lignin (i.e. hydrolases, esterases and oxido-reductases; 2 the key role of lytic polysaccharide monooxygenases (LPMO; 3 the early transcriptional regulation of lignin active peroxidases; 4 the induction of detoxification processes dealing with biomass-derived compounds; and 5 the frequent attachments of the carbohydrate binding module 1 (CBM1 to enzymes from the lignocellulose-responsive genes. Our omics combining methods and related biological findings may contribute to the knowledge of fungal systems biology and facilitate the optimization of fungal enzyme cocktails for various

  16. Veterinary Medicine and Multi-Omics Research for Future Nutrition Targets: Metabolomics and Transcriptomics of the Common Degenerative Mitral Valve Disease in Dogs.

    Science.gov (United States)

    Li, Qinghong; Freeman, Lisa M; Rush, John E; Huggins, Gordon S; Kennedy, Adam D; Labuda, Jeffrey A; Laflamme, Dorothy P; Hannah, Steven S

    2015-08-01

    Canine degenerative mitral valve disease (DMVD) is the most common form of heart disease in dogs. The objective of this study was to identify cellular and metabolic pathways that play a role in DMVD by performing metabolomics and transcriptomics analyses on serum and tissue (mitral valve and left ventricle) samples previously collected from dogs with DMVD or healthy hearts. Gas or liquid chromatography followed by mass spectrophotometry were used to identify metabolites in serum. Transcriptomics analysis of tissue samples was completed using RNA-seq, and selected targets were confirmed by RT-qPCR. Random Forest analysis was used to classify the metabolites that best predicted the presence of DMVD. Results identified 41 known and 13 unknown serum metabolites that were significantly different between healthy and DMVD dogs, representing alterations in fat and glucose energy metabolism, oxidative stress, and other pathways. The three metabolites with the greatest single effect in the Random Forest analysis were γ-glutamylmethionine, oxidized glutathione, and asymmetric dimethylarginine. Transcriptomics analysis identified 812 differentially expressed transcripts in left ventricle samples and 263 in mitral valve samples, representing changes in energy metabolism, antioxidant function, nitric oxide signaling, and extracellular matrix homeostasis pathways. Many of the identified alterations may benefit from nutritional or medical management. Our study provides evidence of the growing importance of integrative approaches in multi-omics research in veterinary and nutritional sciences.

  17. Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases.

    Science.gov (United States)

    Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

    2011-07-01

    Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org.

  18. Determining Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: Part B-Structuromics

    Czech Academy of Sciences Publication Activity Database

    Falk, Martin; Hausmann, M.; Lukášová, Emilie; Biswas, A.; Hildenbrand, G.; Davídková, Marie; Krasavin, E.; Kleibl, Z.; Falková, Iva; Ježková, L.; Štefančíková, Lenka; Ševčík, J.; Hofer, Michal; Bačíková, Alena; Matula, Pavel; Boreyko, A.; Vachelová, Jana; Michaelidesová, Anna; Kozubek, Stanislav

    2014-01-01

    Roč. 24, č. 3 (2014), s. 225-247 ISSN 1045-4403 R&D Projects: GA ČR GBP302/12/G157; GA ČR GAP302/10/1022; GA MŠk LD12039; GA MŠk LD12008; GA MŠk(XE) LM2011019 Institutional support: RVO:68081707 ; RVO:61389005 Keywords : omics * ionizing radiation * low-dose dilemma * biological complexity and variability * higher-order chromatin structure * DNA damage response * formation of chromosomal translocations * confocal microscopy * localization nanoscopy Subject RIV: BO - Biophysics; BO - Biophysics (BFU-R) Impact factor: 1.571, year: 2014

  19. Identifying Health Information Technology Needs of Oncologists to Facilitate the Adoption of Genomic Medicine: Recommendations From the 2016 American Society of Clinical Oncology Omics and Precision Oncology Workshop.

    Science.gov (United States)

    Hughes, Kevin S; Ambinder, Edward P; Hess, Gregory P; Yu, Peter Paul; Bernstam, Elmer V; Routbort, Mark J; Clemenceau, Jean Rene; Hamm, John T; Febbo, Phillip G; Domchek, Susan M; Chen, James L; Warner, Jeremy L

    2017-09-20

    At the ASCO Data Standards and Interoperability Summit held in May 2016, it was unanimously decided that four areas of current oncology clinical practice have serious, unmet health information technology needs. The following areas of need were identified: 1) omics and precision oncology, 2) advancing interoperability, 3) patient engagement, and 4) value-based oncology. To begin to address these issues, ASCO convened two complementary workshops: the Omics and Precision Oncology Workshop in October 2016 and the Advancing Interoperability Workshop in December 2016. A common goal was to address the complexity, enormity, and rapidly changing nature of genomic information, which existing electronic health records are ill equipped to manage. The subject matter experts invited to the Omics and Precision Oncology Workgroup were tasked with the responsibility of determining a specific, limited need that could be addressed by a software application (app) in the short-term future, using currently available genomic knowledge bases. Hence, the scope of this workshop was to determine the basic functionality of one app that could serve as a test case for app development. The goal of the second workshop, described separately, was to identify the specifications for such an app. This approach was chosen both to facilitate the development of a useful app and to help ASCO and oncologists better understand the mechanics, difficulties, and gaps in genomic clinical decision support tool development. In this article, we discuss the key challenges and recommendations identified by the workshop participants. Our hope is to narrow the gap between the practicing oncologist and ongoing national efforts to provide precision oncology and value-based care to cancer patients.

  20. Annual report of the Institute of Physical and Chemical Research, for fiscal 1997

    International Nuclear Information System (INIS)

    1998-01-01

    This annual report are constructed by two volumes: Research subjects of laboratories and research groups and Frontier research program. In the former, research actions of 44 laboratories on Wako Campus, 1 project office of research groups, 6 laboratories of Tsukuba life science center, 1 center and 4 laboratories of RIKEN Harima institute, and scientific and technical services were described. And, actions on 6 kinds of basic science research, 1 research of protein folds research, 4 kinds of research concerning the peaceful use of atomic energy, 1 international collaboration, 2 kinds of development of fundamental technology, 3 kinds of development of computational science and technology, 5 kinds of basic science research on life science, 1 research on synchrotron radiation science, 1 research on synchrotron program and others, 1 research on synchrotron radiation instrumentation, 3 kinds of strategic research program and others, and 1 special contract research were also described in basic science research and others. In the latter, in frontier research program, research actions on 5 laboratories of bio-homeostasis research, 3 laboratories of frontier materials research, 10 laboratories of brain science research, 4 laboratories of photodynamics research, and 4 laboratories of bio-mimetic control research were described. And, actions on 4 laboratories of neuronal function research group, 3 laboratories of neuronal circuit mechanisms research group, 2 laboratories of cognitive brain science group, 2 laboratories of developmental brain science group, 3 laboratories of molecular neuropathology group, 2 laboratories of brainway group, 3 laboratories of brain-style information systems research group, and 3 laboratories of advanced technology development center were described in brain science institute, RIKEN. (G.K.)

  1. An OMIC biomarker detection algorithm TriVote and its application in methylomic biomarker detection.

    Science.gov (United States)

    Xu, Cheng; Liu, Jiamei; Yang, Weifeng; Shu, Yayun; Wei, Zhipeng; Zheng, Weiwei; Feng, Xin; Zhou, Fengfeng

    2018-04-01

    Transcriptomic and methylomic patterns represent two major OMIC data sources impacted by both inheritable genetic information and environmental factors, and have been widely used as disease diagnosis and prognosis biomarkers. Modern transcriptomic and methylomic profiling technologies detect the status of tens of thousands or even millions of probing residues in the human genome, and introduce a major computational challenge for the existing feature selection algorithms. This study proposes a three-step feature selection algorithm, TriVote, to detect a subset of transcriptomic or methylomic residues with highly accurate binary classification performance. TriVote outperforms both filter and wrapper feature selection algorithms with both higher classification accuracy and smaller feature number on 17 transcriptomes and two methylomes. Biological functions of the methylome biomarkers detected by TriVote were discussed for their disease associations. An easy-to-use Python package is also released to facilitate the further applications.

  2. Stemcell Information: SKIP000139 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available es Unknown ... Masayo Takahashi 高橋 政代 Riken Center for Developmental Biology (Riken CDB) 理研発生再生科学総合研究センター ...(理研CDB) Riken Center for Developmental Biology (Riken CDB) 理研発生再生科学総合研究センター (理研CDB) Masayo Takahashi 高橋 政代 N

  3. Stemcell Information: SKIP000137 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available nknown ... Masayo Takahashi 高橋 政代 Riken Center for Developmental Biology (Riken CDB) 理研発生再生科学総合研究センター (理研C...DB) Riken Center for Developmental Biology (Riken CDB) 理研発生再生科学総合研究センター (理研CDB) Masayo Takahashi 高橋 政代 Not A

  4. Database Description - SSBD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available base Description General information of database Database name SSBD Alternative nam...ss 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan, RIKEN Quantitative Biology Center Shuichi Onami E-mail: Database... classification Other Molecular Biology Databases Database classification Dynamic databa...elegans Taxonomy ID: 6239 Taxonomy Name: Escherichia coli Taxonomy ID: 562 Database description Systems Scie...i Onami Journal: Bioinformatics/April, 2015/Volume 31, Issue 7 External Links: Original website information Database

  5. Predicting interactions from mechanistic information: Can omic data validate theories?

    International Nuclear Information System (INIS)

    Borgert, Christopher J.

    2007-01-01

    To address the most pressing and relevant issues for improving mixture risk assessment, researchers must first recognize that risk assessment is driven by both regulatory requirements and scientific research, and that regulatory concerns may expand beyond the purely scientific interests of researchers. Concepts of 'mode of action' and 'mechanism of action' are used in particular ways within the regulatory arena, depending on the specific assessment goals. The data requirements for delineating a mode of action and predicting interactive toxicity in mixtures are not well defined from a scientific standpoint due largely to inherent difficulties in testing certain underlying assumptions. Understanding the regulatory perspective on mechanistic concepts will be important for designing experiments that can be interpreted clearly and applied in risk assessments without undue reliance on extrapolation and assumption. In like fashion, regulators and risk assessors can be better equipped to apply mechanistic data if the concepts underlying mechanistic research and the limitations that must be placed on interpretation of mechanistic data are understood. This will be critically important for applying new technologies to risk assessment, such as functional genomics, proteomics, and metabolomics. It will be essential not only for risk assessors to become conversant with the language and concepts of mechanistic research, including new omic technologies, but also, for researchers to become more intimately familiar with the challenges and needs of risk assessment

  6. Multiomics Data Triangulation for Asthma Candidate Biomarkers and Precision Medicine.

    Science.gov (United States)

    Pecak, Matija; Korošec, Peter; Kunej, Tanja

    2018-06-01

    Asthma is a common complex disorder and has been subject to intensive omics research for disease susceptibility and therapeutic innovation. Candidate biomarkers of asthma and its precision treatment demand that they stand the test of multiomics data triangulation before they can be prioritized for clinical applications. We classified the biomarkers of asthma after a search of the literature and based on whether or not a given biomarker candidate is reported in multiple omics platforms and methodologies, using PubMed and Web of Science, we identified omics studies of asthma conducted on diverse platforms using keywords, such as asthma, genomics, metabolomics, and epigenomics. We extracted data about asthma candidate biomarkers from 73 articles and developed a catalog of 190 potential asthma biomarkers (167 human, 23 animal data), comprising DNA loci, transcripts, proteins, metabolites, epimutations, and noncoding RNAs. The data were sorted according to 13 omics types: genomics, epigenomics, transcriptomics, proteomics, interactomics, metabolomics, ncRNAomics, glycomics, lipidomics, environmental omics, pharmacogenomics, phenomics, and integrative omics. Importantly, we found that 10 candidate biomarkers were apparent in at least two or more omics levels, thus promising potential for further biomarker research and development and precision medicine applications. This multiomics catalog reported herein for the first time contributes to future decision-making on prioritization of biomarkers and validation efforts for precision medicine in asthma. The findings may also facilitate meta-analyses and integrative omics studies in the future.

  7. BDML Metadata: 232 [SSBD[Archive

    Lifescience Database Archive (English)

    Full Text Available 22-efb1-4a87-93b7-0b7216a58137 0.105 x 0.105 x 0.5 (micrometer), 40 (second) http://ssbd.qbic.riken.jp/data/...source/Ce_KK_P002/RNAi_T26G10.1_070222_01/ http://ssbd.qbic.riken.jp/data/bdml/Ce..._KK_P002/RNAi_T26G10.1_070222_01.bdml0.15.xml http://ssbd.qbic.riken.jp/data/pdpml/Ce_KK_P002.pdpml0.05.xml ...http://ssbd.qbic.riken.jp/search/45ebf022-efb1-4a87-93b7-0b7216a58137/ http://ssbd.qbic.riken.jp/omero/webclient/?show=dataset-166 ...

  8. BDML Metadata: 171 [SSBD[Archive

    Lifescience Database Archive (English)

    Full Text Available NC-SA 0.180 ddc4bac7-2646-4717-a00a-4daff073490b 0.105 x 0.105 x 0.5 (micrometer), 40 (second) http://ssbd.qbic.riken.jp/data.../source/Ce_KK_P002/RNAi_R10E4.4_061107_01.zip http://ssbd.qbic.riken.jp/data.../bdml/Ce_KK_P002/RNAi_R10E4.4_061107_01.bdml0.18.xml http://ssbd.qbic.riken.jp/data/pdpml/Ce_KK_...P002.pdpml0.06.xml http://ssbd.qbic.riken.jp/search/ddc4bac7-2646-4717-a00a-4daff073490b/ http://ssbd.qbic.riken.jp/omero/webclient/?show=dataset-87 ...

  9. BDML Metadata: 234 [SSBD[Archive

    Lifescience Database Archive (English)

    Full Text Available 9a-06cf-4f99-a337-01b1f9166310 0.105 x 0.105 x 0.5 (micrometer), 40 (second) http://ssbd.qbic.riken.jp/data/...source/Ce_KK_P002/RNAi_T26G10.1_070920_01/ http://ssbd.qbic.riken.jp/data/bdml/Ce..._KK_P002/RNAi_T26G10.1_070920_01.bdml0.15.xml http://ssbd.qbic.riken.jp/data/pdpml/Ce_KK_P002.pdpml0.05.xml ...http://ssbd.qbic.riken.jp/search/24115f9a-06cf-4f99-a337-01b1f9166310/ http://ssbd.qbic.riken.jp/omero/webclient/?show=dataset-167 ...

  10. The Medical Science DMZ.

    Science.gov (United States)

    Peisert, Sean; Barnett, William; Dart, Eli; Cuff, James; Grossman, Robert L; Balas, Edward; Berman, Ari; Shankar, Anurag; Tierney, Brian

    2016-11-01

    We describe use cases and an institutional reference architecture for maintaining high-capacity, data-intensive network flows (e.g., 10, 40, 100 Gbps+) in a scientific, medical context while still adhering to security and privacy laws and regulations. High-end networking, packet filter firewalls, network intrusion detection systems. We describe a "Medical Science DMZ" concept as an option for secure, high-volume transport of large, sensitive data sets between research institutions over national research networks. The exponentially increasing amounts of "omics" data, the rapid increase of high-quality imaging, and other rapidly growing clinical data sets have resulted in the rise of biomedical research "big data." The storage, analysis, and network resources required to process these data and integrate them into patient diagnoses and treatments have grown to scales that strain the capabilities of academic health centers. Some data are not generated locally and cannot be sustained locally, and shared data repositories such as those provided by the National Library of Medicine, the National Cancer Institute, and international partners such as the European Bioinformatics Institute are rapidly growing. The ability to store and compute using these data must therefore be addressed by a combination of local, national, and industry resources that exchange large data sets. Maintaining data-intensive flows that comply with HIPAA and other regulations presents a new challenge for biomedical research. Recognizing this, we describe a strategy that marries performance and security by borrowing from and redefining the concept of a "Science DMZ"-a framework that is used in physical sciences and engineering research to manage high-capacity data flows. By implementing a Medical Science DMZ architecture, biomedical researchers can leverage the scale provided by high-performance computer and cloud storage facilities and national high-speed research networks while preserving privacy and

  11. Unveiling Microbial Carbon Cycling Processes in Key U.S. Soils using ''Omics''

    Energy Technology Data Exchange (ETDEWEB)

    Myrold, David D. [Oregon State Univ., Corvallis, OR (United States); Bottomely, Peter J. [Oregon State Univ., Corvallis, OR (United States); Jumpponen, Ari [Kansas State Univ., Manhattan, KS (United States); Rice, Charles W. [Kansas State Univ., Manhattan, KS (United States); Zeglin, Lydia H. [Kansas State Univ., Manhattan, KS (United States); David, Maude M. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Jansson, Janet K. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Prestat, Emmanuel [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Hettich, Robert L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2014-09-17

    Soils process and store large amounts of C; however, considerable uncertainty still exists about the details of that influence microbial partitioning of C into soil C pools, and what are the main influential forces that control the fraction of the C input that is stabilized. The soil microbial community is genotypically and phenotypically diverse. Despite our ability to predict the kinds of regional environmental changes that will accompany global climate change, it is not clear how the microbial community will respond to climate-induced modification of precipitation and inter-precipitation intervals, and if this response will affect the fate of C deposited into soil by the local plant community. Part of this uncertainty lies with our ignorance of how the microbial community adapts genotypically and physiologically to changes in soil moisture brought about by shifts in precipitation. Our overarching goal is to harness the power of multiple meta-omics tools to gain greater understanding of the functioning of whole-soil microbial communities and their role in C cycling. We will do this by meeting the following three objectives: 1. Further develop and optimize a combination of meta-omics approaches to study how environmental factors affect microbially-mediated C cycling processes. 2. Determine the impacts of long-term changes in precipitation timing on microbial C cycling using an existing long-term field manipulation of a tallgrass prairie soil. 3. Conduct laboratory experiments that vary moisture and C inputs to confirm field observations of the linkages between microbial communities and C cycling processes. We took advantage of our state-of-the-art expertise in community “omics” to better understand the functioning soil C cycling within the Great Prairie ecosystem, including our ongoing Konza Prairie soil metagenome flagship project at JGI and the unique rainfall manipulation plots (RaMPs) established at this site more than a decade ago. We employed a systems

  12. Characterization of Chinese Hamster Ovary Cells Producing Coagulation Factor VIII Using Multi-omics Tools

    DEFF Research Database (Denmark)

    Kaas, Christian Schrøder

    The first public draft of a genome from Chinese hamster ovary (CHO) cells was published in 2011, an entire decade after the first draft of the human genome. This publication of a relevant CHO reference genome, in combination with the fact that the cost for DNA sequencing has dropped more than 10...... using omics tools. A wide range of methods were applied including whole-genome sequencing, targeted genome sequencing, mRNA sequencing, miRNA sequencing and mass spectrometry based shotgun proteomics on a number of clones in order to get a more holistic picture of the inner workings of these CHO...... transfectants. From the whole-genome sequencing of two CHO genomes (CHO DXB11 and the FVIII producing transfectant: F435) it was observed that roughly 20% of the genes in the genome were haploid and roughly 10% had a copy number of three or higher indicating extensive rearrangements compared to the Chinese...

  13. Stemcell Information: SKIP000627 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ... RIKEN BioResource Center 理化学研究所バイオリソースセンター RIKEN BioResource Center 理化学...研究所バイオリソースセンター Available RIKEN BioResource Center 理化学研究所バイオリソースセンター http://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HPS0332&type=1 ...

  14. Nematode-bacterium symbioses--cooperation and conflict revealed in the "omics" age.

    Science.gov (United States)

    Murfin, Kristen E; Dillman, Adler R; Foster, Jeremy M; Bulgheresi, Silvia; Slatko, Barton E; Sternberg, Paul W; Goodrich-Blair, Heidi

    2012-08-01

    Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for the investigation of host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a variety of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved, their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we discuss the importance and diversity of nematodes, "omics"' studies in nematode-bacterial systems, and the wider implications of the findings.

  15. Multi-omics approach identifies molecular mechanisms of plant-fungus mycorrhizal interaction

    Directory of Open Access Journals (Sweden)

    Peter E Larsen

    2016-01-01

    Full Text Available In mycorrhizal symbiosis, plant roots form close, mutually beneficial interactions with soil fungi. Before this mycorrhizal interaction can be established however, plant roots must be capable of detecting potential beneficial fungal partners and initiating the gene expression patterns necessary to begin symbiosis. To predict a plant root – mycorrhizal fungi sensor systems, we analyzed in vitro experiments of Populus tremuloides (aspen tree and Laccaria bicolor (mycorrhizal fungi interaction and leveraged over 200 previously published transcriptomic experimental data sets, 159 experimentally validated plant transcription factor binding motifs, and more than 120-thousand experimentally validated protein-protein interactions to generate models of pre-mycorrhizal sensor systems in aspen root. These sensor mechanisms link extracellular signaling molecules with gene regulation through a network comprised of membrane receptors, signal cascade proteins, transcription factors, and transcription factor biding DNA motifs. Modeling predicted four pre-mycorrhizal sensor complexes in aspen that interact with fifteen transcription factors to regulate the expression of 1184 genes in response to extracellular signals synthesized by Laccaria. Predicted extracellular signaling molecules include common signaling molecules such as phenylpropanoids, salicylate, and, jasmonic acid. This multi-omic computational modeling approach for predicting the complex sensory networks yielded specific, testable biological hypotheses for mycorrhizal interaction signaling compounds, sensor complexes, and mechanisms of gene regulation.

  16. Stemcell Information: SKIP000134 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available human basic FGF ... Yes Unknown ... Masayo Takahashi 高橋 政代 Riken Center for Developmental Biology... (Riken CDB) 理研発生再生科学総合研究センター (理研CDB) Riken Center for Developmental Biology

  17. Environmental "Omics" of International Space Station: Insights, Significance, and Consequences

    Science.gov (United States)

    Venkateswaran, Kasthuri

    2016-07-01

    The NASA Space Biology program funded two multi-year studies to catalogue International Space Station (ISS) environmental microbiome. The first Microbial Observatory (MO) experiment will generate a microbial census of the ISS surfaces and atmosphere using advanced molecular microbial community analysis "omics" techniques, supported by traditional culture-based methods and state-of-the art molecular techniques. The second MO experiment will measure presence of viral and select bacterial and fungal pathogens on ISS surfaces and correlate their presence on crew. The "omics" methodologies of the MO experiments will serve as the foundation for an extensive microbial census, offering significant insight into spaceflight-induced changes in the populations of beneficial and potentially harmful microbes. The safety of crewmembers and the maintenance of hardware are the primary goals for monitoring microorganisms in this closed habitat. The statistical analysis of the ISS microbiomes showed that three bacterial phyla dominated both in ISS and Earth cleanrooms, but varied in their abundances. While members of Actinobacteria were predominant on ISS, Proteobacteria dominated the Earth cleanrooms. Alpha diversity estimators indicated a significant drop in viable microbial diversity. To better characterize the shared community composition among samples, beta-diversity metrics analysis were conducted. At the bacterial species level characterization, the microbial community composition is strongly associated with sampling site. Results of the study indicate significant differences between ISS and Earth cleanroom microbiomes in terms of community structure and composition. Bacterial strains isolated from ISS surfaces were also tested for their resistance to nine antibiotics using conventional disc method and Vitek 2 system. Most of the Staphylococcus aureus strains were resistant to penicillin. Five strains were specifically resistant to erythromycin and the ermA gene was also

  18. Proceedings of RIKEN BNL Research Center Workshop: P- and CP-odd Effects in Hot and Dense Matter

    Energy Technology Data Exchange (ETDEWEB)

    Deshpande, A.; Fukushima, K.; Kharzeev, D.; Warringa, H.; Voloshin, S.

    2010-04-26

    This volume contains the proceedings of the RBRC/CATHIE workshop on 'P- and CP-odd Effects in Hot and Dense Matter' held at the RIKEN-BNL Research Center on April 26-30, 2010. The workshop was triggered by the experimental observation of charge correlations in heavy ion collisions at RHIC, which were predicted to occur due to local parity violation (P- and CP-odd fluctuations) in hot and dense QCD matter. This experimental result excited a significant interest in the broad physics community, inspired a few alternative interpretations, and emphasized the need for a deeper understanding of the role of topology in QCD vacuum and in hot and dense quark-gluon matter. Topological effects in QCD are also closely related to a number of intriguing problems in condensed matter physics, cosmology and astrophysics. We therefore felt that a broad cross-disciplinary discussion of topological P- and CP-odd effects in various kinds of matter was urgently needed. Such a discussion became the subject of the workshop. Specific topics discussed at the workshop include the following: (1) The current experimental results on charge asymmetries at RHIC and the physical interpretations of the data; (2) Quantitative characterization of topological effects in QCD matter including both analytical (perturbative and non-perturbative using gauge/gravity duality) and numerical (lattice-QCD) calculations; (3) Topological effects in cosmology of the Early Universe (including baryogenesis and dark energy); (4) Topological effects in condensed matter physics (including graphene and superfiuids); and (5) Directions for the future experimental studies of P- and CP-odd effects at RHIC and elsewhere. We feel that the talks and intense discussions during the workshop were extremely useful, and resulted in new ideas in both theory and experiment. We hope that the workshop has contributed to the progress in understanding the role of topology in QCD and related fields. We thank all the speakers and

  19. Proceedings of RIKEN BNL Research Center Workshop: P- and CP-odd Effects in Hot and Dense Matter

    International Nuclear Information System (INIS)

    Deshpande, A.; Fukushima, K.; Kharzeev, D.; Warringa, H.; Voloshin, S.

    2010-01-01

    This volume contains the proceedings of the RBRC/CATHIE workshop on 'P- and CP-odd Effects in Hot and Dense Matter' held at the RIKEN-BNL Research Center on April 26-30, 2010. The workshop was triggered by the experimental observation of charge correlations in heavy ion collisions at RHIC, which were predicted to occur due to local parity violation (P- and CP-odd fluctuations) in hot and dense QCD matter. This experimental result excited a significant interest in the broad physics community, inspired a few alternative interpretations, and emphasized the need for a deeper understanding of the role of topology in QCD vacuum and in hot and dense quark-gluon matter. Topological effects in QCD are also closely related to a number of intriguing problems in condensed matter physics, cosmology and astrophysics. We therefore felt that a broad cross-disciplinary discussion of topological P- and CP-odd effects in various kinds of matter was urgently needed. Such a discussion became the subject of the workshop. Specific topics discussed at the workshop include the following: (1) The current experimental results on charge asymmetries at RHIC and the physical interpretations of the data; (2) Quantitative characterization of topological effects in QCD matter including both analytical (perturbative and non-perturbative using gauge/gravity duality) and numerical (lattice-QCD) calculations; (3) Topological effects in cosmology of the Early Universe (including baryogenesis and dark energy); (4) Topological effects in condensed matter physics (including graphene and superfiuids); and (5) Directions for the future experimental studies of P- and CP-odd effects at RHIC and elsewhere. We feel that the talks and intense discussions during the workshop were extremely useful, and resulted in new ideas in both theory and experiment. We hope that the workshop has contributed to the progress in understanding the role of topology in QCD and related fields. We thank all the speakers and

  20. Stemcell Information: SKIP000827 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ... RIKEN BioResource Center 理化学研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Ava...ilable RIKEN BioResource Center 理化学研究所バイオリソースセンター http://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HPS0332&type=1 ...

  1. Stemcell Information: SKIP000633 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Yes ... RIKEN BioResource Center 理化学研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター ... Avai...lable RIKEN BioResource Center 理化学研究所バイオリソースセンター http://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HPS0337&type=1 ...

  2. Stemcell Information: SKIP000632 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Yes ... RIKEN BioResource Center 理化学研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター ... Avai...lable RIKEN BioResource Center 理化学研究所バイオリソースセンター http://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HPS0337&type=1 ...

  3. Stemcell Information: SKIP000614 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available a patient.Amyotrophic lateral sclerosis, Familial type. ... 疾患特異的iPS細胞株。家族性筋萎縮性側索硬化症患者由来。 human ES-like Resear...sclerosis, Familial type ... -- -- Japanese Japanese No No Disease specific iPS cell line derived from...g/ml human bFGF ... 3% Unknown ... RIKEN BRC 理研BRC RIKEN BRC 理研BRC ... Available RIKEN BRC 理研BRC http://www.brc.riken.jp/lab/cell/english/ ...

  4. Stemcell Information: SKIP000634 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Yes ... RIKEN BioResource Center 理化学研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター ... Avai...lable RIKEN BioResource Center 理化学研究所バイオリソースセンター http://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HPS0337&type=1 ...

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    Full Text Available Y-NC-SA 0.150 d169c9a9-4197-416e-9079-f35442f2448c 0.105 x 0.105 x 0.5 (micrometer), 40 (second) http://ssbd.qbic.riken.jp/data.../source/Ce_KK_P002/RNAi_C29E4.8_040610_02/ http://ssbd.qbic.riken.jp/data.../bdml/Ce_KK_P002/RNAi_C29E4.8_040610_02.bdml0.15.xml http://ssbd.qbic.riken.jp/data/pdpml/Ce_KK_P...002.pdpml0.05.xml http://ssbd.qbic.riken.jp/search/d169c9a9-4197-416e-9079-f35442f2448c/ http://ssbd.qbic.riken.jp/omero/webclient/?show=dataset-26 ...

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    Full Text Available NC-SA 0.150 dcad3847-c87f-462d-9c90-6c120cdd3cab 0.105 x 0.105 x 0.5 (micrometer), 40 (second) http://ssbd.qbic.riken.jp/data.../source/Ce_KK_P002/RNAi_T12D8.7_070220_02/ http://ssbd.qbic.riken.jp/data.../bdml/Ce_KK_P002/RNAi_T12D8.7_070220_02.bdml0.15.xml http://ssbd.qbic.riken.jp/data/pdpml/Ce_KK_P00...2.pdpml0.05.xml http://ssbd.qbic.riken.jp/search/dcad3847-c87f-462d-9c90-6c120cdd3cab/ http://ssbd.qbic.riken.jp/omero/webclient/?show=dataset-155 ...

  12. Nutrigenomics : exploiting systems biology in the nutrition and health arena

    NARCIS (Netherlands)

    Ommen, B. van; Stierum, R.

    2002-01-01

    Nutritional sciences are discovering the application of the so-called 'omics' sciences. Propelled by the recent unravelling of the human genome and the coinciding technological developments, genotyping, transcriptomics, proteomics and metabolomics are now available to nutritional research. In the

  13. Stemcell Information: SKIP000136 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available iology (Riken CDB) 理研発生再生科学総合研究センター (理研CDB) Masayo Takahashi 高橋 政代 Not Available Riken BRC 理研BRC http://www.brc.riken.jp/lab/cell/english/patient_specific_ips.shtml ...

  14. Stemcell Information: SKIP000135 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available iology (Riken CDB) 理研発生再生科学総合研究センター (理研CDB) Masayo Takahashi 高橋 政代 Not Available Riken BRC 理研BRC http://www.brc.riken.jp/lab/cell/english/patient_specific_ips.shtml ...

  15. Multi-omic profiling of EPO-producing CHO cell panel reveals metabolic adaptation to heterologous protein production

    DEFF Research Database (Denmark)

    Ley, Daniel; Kazemi Seresht, Ali; Engmark, Mikael

    The Chinese hamster ovary (CHO) cell line is the predominant mammalian cell factory for production of therapeutic glycoproteins. In this work, we aimed to study bottlenecks in the secretory pathway associated with the production of human erythropoietin (EPO) in CHO cells. In connection to this, we...... discovered indications of metabolic adaptation of the amino acid catabolism in favor of heterologous protein production. We established a panel of stably EPO expressing CHO-K1 clones spanning a 25-fold productivity range and characterized the clones in batch and chemostat cultures. For this, we employed...... a multi-omic physiological characterization including metabolic foot printing of amino acids, metabolite fingerprinting of glycolytic intermediates, NAD(P)H-/NAD(P)+ and adenosine nucleotide phosphates. We used qPCR, qRT-PCR, western blots and Affymetrix CHO microarrays to assess EPO gene copy numbers...

  16. Application of Omics Technologies in the System of Sports Training

    Directory of Open Access Journals (Sweden)

    E.A. Semenova

    2017-06-01

    Full Text Available Deciphering the human genome, and further development of omics technologies, have opened new opportunities in studying the molecular mechanisms underlying the sport success. According to modern concepts of functional genomics, it is believed that individual differences in the degree of development of physical and mental qualities, as well as in the susceptibility to different diseases of athletes are largely due to DNA polymorphisms. Genetic markers associated with the development and manifestation of physical qualities (speed, strength, endurance, agility, flexibility can be used in the sports selection system, to clarify sports specialization and to optimize the training process. Other molecular markers (methyl groups, trans­cripts, telomerase activity, telomeres, circulating DNA, metabolites, proteins, etc. in addition to predicting athletic performance, allow assessing the current functional state of the athlete, including the phenomenon of overtraining. The purpose of this review is to provide data on the use of genomic, epigenetic, trans­criptomic, proteomic and metabolic methods in sports talent identification, assessing the current functional status of athletes and in the pres­cription of personal training and nutrition programs. Future research, including multicentre genome-wide association studies and whole-genome sequencing in large cohorts of athletes with further validation and replication, will substantially contribute to the discovery of large numbers of the causal genetic variants (mutations and DNA polymorphisms that would partly explain the heritability of athlete status and related phenotypes.

  17. Stemcell Information: SKIP000624 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available RIKEN BioResource Center 理化学研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Available RIKEN BioResource Center 理化学

  18. Stemcell Information: SKIP000807 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available tia of Alzheimers type. Order Form to RIKEN BRC (C-0042, C-0057, C-0007). 疾患特異的iPS細胞株。アルツハイマー型認知症患者由来。ガラス化法(...ers type - ... -- Male Japanese 日本人 No No Disease specific iPS cell line derived from a patient : Demen...enter (RIKEN ... BRC 理化学研究所バイオリソースセンター Available RIKEN BioResouce Center (RIKEN ... BRC) 理化学研究所バイオリソースセンター http://www2.brc.riken.jp/lab/cel...l/detail.cgi?cell_no=HPS0059&type=1 ...

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    Full Text Available -NC-SA 0.180 78e79e34-b7fd-47f7-a2f2-8c8732f1140e 0.105 x 0.105 x 0.5 (micrometer), 40 (second) http://ssbd.qbic.riken.jp/data.../source/Ce_KK_P002/RNAi_R12B2.4_040819_01.zip http://ssbd.qbic.riken.jp/data.../bdml/Ce_KK_P002/RNAi_R12B2.4_040819_01.bdml0.18.xml http://ssbd.qbic.riken.jp/data/pdpml/Ce_KK..._P002.pdpml0.06.xml http://ssbd.qbic.riken.jp/search/78e79e34-b7fd-47f7-a2f2-8c8732f1140e/ http://ssbd.qbic.riken.jp/omero/webclient/?show=dataset-89 ...

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    Lifescience Database Archive (English)

    Full Text Available NC-SA 0.150 d525ac20-97f8-4e99-a9d1-3f44440cbb2c 0.105 x 0.105 x 0.5 (micrometer), 40 (second) http://ssbd.qbic.riken.jp/data.../source/Ce_KK_P002/RNAi_W07B3.2_040928_01/ http://ssbd.qbic.riken.jp/data.../bdml/Ce_KK_P002/RNAi_W07B3.2_040928_01.bdml0.15.xml http://ssbd.qbic.riken.jp/data/pdpml/Ce_KK_P00...2.pdpml0.05.xml http://ssbd.qbic.riken.jp/search/d525ac20-97f8-4e99-a9d1-3f44440cbb2c/ http://ssbd.qbic.riken.jp/omero/webclient/?show=dataset-169 ...

  9. Macromycetes of oak-lime-hornbeam woods in the Niepołomice Forest near Kraków (S Poland - monitoring studies

    Directory of Open Access Journals (Sweden)

    Władysława Wojewoda

    2014-08-01

    Full Text Available In the years 1994-1996 studies on macromycetes of the Niepołomice Forest near Kraków were made in four plots designated in deciduous forests (Tilio-Carpinetum stachyetosum with a population of Carpinus betulus, Quercus robur and Tilia cordata (the size of each plot was 1000 m2. The observations were made through an international project "Mycological monitoring in European oak forests". As many as 274 species were recorded, including 234 saprobic, 33 mycorrhizal, and 7 parasitic fungi. Moreover, 15 species of fungi are connected with oak, 24 species of fungi are threatened, and 16 species are new to Poland.

  10. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP ON RHIC SPIN PHYSICS III AND IV, POLARIZED PARTONS AT HIGH Q2 REGION (VOLUME 31)

    International Nuclear Information System (INIS)

    BUNCE, G.; VIGDOR, S.

    2001-01-01

    International workshop on II Polarized Partons at High Q2 region 11 was held at the Yukawa Institute for Theoretical Physics, Kyoto University, Kyoto, Japan on October 13-14, 2000, as a satellite of the international conference ''SPIN 2000'' (Osaka, Japan, October 16-21,2000). This workshop was supported by RIKEN (The Institute of Physical and Chemical Research) and by Yukawa Institute. The scientific program was focused on the upcoming polarized collider RHIC. The workshop was also an annual meeting of RHIC Spin Collaboration (RSC). The number of participants was 55, including 28 foreign visitors and 8 foreign-resident Japanese participants, reflecting the international nature of the RHIC spin program. At the workshop there were 25 oral presentations in four sessions, (1) RHIC Spin Commissioning, (2) Polarized Partons, Present and Future, (3) New Ideas on Polarization Phenomena, (4) Strategy for the Coming Spin Running. In (1) the successful polarized proton commissioning and the readiness of the accelerator for the physics program impressed us. In (2) and (3) active discussions were made on the new structure function to be firstly measured at RHIC, and several new theoretical ideas were presented. In session (4) we have established a plan for the beam time requirement toward the first collision of polarized protons. These proceedings include the transparencies presented at the workshop. The discussion on ''Strategy for the Coming Spin Running'' was summarized by the chairman of the session, S. Vigdor and G. Bunce

  11. BDML Metadata: 58 [SSBD[Archive

    Lifescience Database Archive (English)

    Full Text Available NC-SA 0.150 358e41f1-9536-4fc5-93cc-9a38a0b3d4b9 0.105 x 0.105 x 0.5 (micrometer), 40 (second) http://ssbd.qbic.riken.jp/data.../source/Ce_KK_P002/RNAi_C32A3.1_061221_02/ http://ssbd.qbic.riken.jp/data.../bdml/Ce_KK_P002/RNAi_C32A3.1_061221_02.bdml0.15.xml http://ssbd.qbic.riken.jp/data/pdpml/Ce_KK_P00...2.pdpml0.05.xml http://ssbd.qbic.riken.jp/search/358e41f1-9536-4fc5-93cc-9a38a0b3d4b9/ http://ssbd.qbic.riken.jp/omero/webclient/?show=dataset-29 ...

  12. PROCEEDINGS OF RIKEN BNL RESEARCH CENTER WORKSHOP, VOLUME 57, HIGH PT PHYSICS AT RHIC, DECEMBER 2-6, 2003

    Energy Technology Data Exchange (ETDEWEB)

    Kretzer, Stefan; Venugopalan, Raju; Vogelsang, Werner

    2004-02-18

    The AuAu, dAu, and pp collision modes of the RHIC collider at BNL have led to the publication of exciting high p{perpendicular} particle production data. There have also been two physics runs with polarized protons, and preliminary results on the double-spin asymmetry for pion production had been presented very recently. The ontological questions behind these measurements are fascinating: Did RHIC collisions create a Quark-Gluon-Plasma phase and did they verify the Color Glass Condensate as the high energy limit of QCD? Will the Spin Crisis finally be resolved in terms of gluon polarization and what new surprises are we yet to meet for Transverse Spin? Phenomena related to sub-microscopic questions as important as these call for interpretations that are footed in solid theory. At large p{perpendicular}, perturbative concepts are legitimately expected to provide useful approaches. The corresponding hard parton dynamics are, in several ways, key to unraveling the initial or final state and collisional phase of hard scattering events in vacuum as well as in hot or cold nuclear matter. Before the advent of RHIC data, a RIKEN-BNL workshop had been held at BNL in March 1999 on ''Hard Parton Physics in High Energy Nuclear Collisions''. The 2003 workshop on ''High p{perpendicular} Physics at RHIC'' was a logical continuation of this previous workshop. It gave the opportunity to revisit the 1999 expectations in the light of what has been found in the meantime and, at the same time, to critically discuss the underlying theoretical concepts. We brought together theorists who have done seminal work on the foundations of parton phenomenology in field theory, with theorists and experimentalists who are presently working on RHIC phenomenology. The participants were both from a high-energy physics and nuclear physics background and it remains only to be said here that this chemistry worked perfectly and the workshop was a great success.

  13. Update History of This Database - SSBD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us SSBD Update History of This Database Date Update contents 2016/07/25 SSBD English archive si...tion Download License Update History of This Database Site Policy | Contact Us Update History of This Database - SSBD | LSDB Archive ... ...te is opened. 2013/09/03 SSBD ( http://ssbd.qbic.riken.jp/ ) is opened. About This Database Database Descrip

  14. Stemcell Information: SKIP000238 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 2-Mercaptoethanol+5ng/mL human bFGF ... Riken BioResource Center 理化学研究所バイオリソースセンター ...Riken BioResource Center 理化学研究所バイオリソースセンター Available Riken BioResource Center 理化学

  15. Stemcell Information: SKIP000864 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available aptoethanol+5ng/ml human bFGF ... 3% Negative ... RIKEN BioResource center 理化学...研究所バイオリソースセンター RIKEN BioResource center 理化学研究所バイオリソースセンター Available RIKEN BioResource center 理化学

  16. Stemcell Information: SKIP000628 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available Mercaptoethanol+5ng/ml human bFGF ... 5% Negative ... RIKEN BioResource Center 理化学研究所バイオリソ...ースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Available RIKEN BioResource Center 理化学

  17. Shikimic acid production in Escherichia coli: From classical metabolic engineering strategies to omics applied to improve its production

    Directory of Open Access Journals (Sweden)

    Juan Andrés Martínez

    2015-09-01

    Full Text Available Shikimic acid (SA is an intermediate of the SA pathway that is present in bacteria and plants. SA has gained great interest because it is a precursor in the synthesis of the drug oseltamivir phosphate (OSF, an efficient inhibitor of the neuraminidase enzyme of diverse seasonal influenza viruses, the avian influenza virus H5N1, and the human influenza virus H1N1. For the purposes of OSF production, SA is extracted from the pods of Chinese star anise plants (Illicium spp., yielding up to 17% of SA (dry basis content. The high demand for OSF necessary to manage a major influenza outbreak is not adequately met by industrial production using SA from plants sources. As the SA pathway is present in the model bacteria Escherichia coli, several intuitive metabolically engineered strains have been applied for its successful overproduction by biotechnological processes, resulting in strains producing up to 71 g/L of SA, with high conversion yields of up to 0.42 (mol SA/mol Glc, in both batch and fed-batch cultures using complex fermentation broths, including glucose as a carbon source and yeast extract. Global transcriptomic analyses have been performed in SA producing strains, resulting in the identification of possible key target genes for the design of a rational strain improvement strategy. Because possible target genes are involved in the transport, catabolism and interconversion of different carbon sources and metabolic intermediates outside the central carbon metabolism and SA pathways, as genes involved in diverse cellular stress responses, the development of rational cellular strain improvement strategies based on omics data constitutes a challenging task to improve SA production in currently overproducing engineered strains. In this review, we discuss the main metabolic engineering strategies that have been applied for the development of efficient SA producing strains, as the perspective of omics analysis has focused on further strain improvement

  18. Personalized Medicine Applied to Forensic Sciences: New Advances and Perspectives for a Tailored Forensic Approach.

    Science.gov (United States)

    Santurro, Alessandro; Vullo, Anna Maria; Borro, Marina; Gentile, Giovanna; La Russa, Raffaele; Simmaco, Maurizio; Frati, Paola; Fineschi, Vittorio

    2017-01-01

    Personalized medicine (PM), included in P5 medicine (Personalized, Predictive, Preventive, Participative and Precision medicine) is an innovative approach to the patient, emerging from the need to tailor and to fit the profile of each individual. PM promises to dramatically impact also on forensic sciences and justice system in ways we are only beginning to understand. The application of omics (genomic, transcriptomics, epigenetics/imprintomics, proteomic and metabolomics) is ever more fundamental in the so called "molecular autopsy". Emerging fields of interest in forensic pathology are represented by diagnosis and detection of predisposing conditions to fatal thromboembolic and hypertensive events, determination of genetic variants related to sudden death, such as congenital long QT syndromes, demonstration of lesions vitality, identification of biological matrices and species diagnosis of a forensic trace on crime scenes without destruction of the DNA. The aim of this paper is to describe the state-of-art in the application of personalized medicine in forensic sciences, to understand the possibilities of integration in routine investigation of these procedures with classical post-mortem studies and to underline the importance of these new updates in medical examiners' armamentarium in determining cause of death or contributing factors to death. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  19. Stemcell Information: SKIP000635 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available sic FGF ... 5% Negative ... Yes ... Yoshihira ... Matsumoto 松本 佳久 Kyoto University 京都大学 再生医科学研究所 RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター ...Available RIKEN BioResource Center 理化学研究所バイオリソースセンター http://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HP

  20. Stemcell Information: SKIP000630 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available nol+5ng/ml human bFGF ... 5% Negative ... Yes ... RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター ... Available RIKEN BioResource Center 理化学研究

  1. Stemcell Information: SKIP000631 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available nol+5ng/ml human bFGF ... 5% Negative ... Yes ... RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター ... Available RIKEN BioResource Center 理化学研究

  2. Overview of the 3rd phase crossover research on migration of radionuclides in biosphere

    International Nuclear Information System (INIS)

    Uchida, Shigeo; Amano, Hikaru; Chiba, Masaru; Hisamatsu, Shun'ichi; Enomoto, Shuichi; Matsumoto, Shiro

    2003-01-01

    In 1991, we started a series of projects in Nuclear Energy Generic Crossover Research, which is known as ''Crossover Research (CR)''. This 1st phase was successfully finished with the active cooperation of five organizations: Japan Atomic Energy Research Institute (JAERI), Meteorological Research Institute (MRI), National Institute of Radiological Sciences (NIRS), the Institute of Physical and Chemical Research (RIKEN) and Power Reactor and Nuclear Fuel Development Corporation (PNC). Subsequently we carried out the 2nd phase of CR (1996-1998). A new member, Institute for Environmental Sciences (IES) participated from this phase. In the 3rd phase CR, a project on ''Development of a dynamic transfer model of radionuclides in the soil ecosphere'', is currently being promoted (1999-2003). The following five researches are carried out in this project. (1) Research into the forms of existence of nuclide and their change in the soil (NIRS and JAERI), (2) Research into the transition behavior of radionuclides in plants (IES, RIKEN and NIRS), (3) Research into the relation to the microorganism and on environmental remediation (RIKEN, JAERI and NIRS), (4) Research on the migration of radionuclides from atmosphere to soil and plant (MRI and JAERI), and (5) Database construction on transfer parameters (JAERI, NIRS and MRI). Then, JAERI, MRI and NIRS are working on the development of a dynamic transfer model for radionuclides on the basis of a gained knowledge about the environmental behavior with the cooperation of universities, etc. The dynamic transfer model developed in this project is effective not only for Japan, but also for the Southeast Asian countries. Besides, this model is capable of predicting the behavior of materials that are harmful to the environment, i.e. hazardous heavy metals discharged in the soil ecosphere. (author)

  3. Evaluating biological variation in non-transgenic crops: executive summary from the ILSI Health and Environmental Sciences Institute workshop, November 16-17, 2009, Paris, France

    DEFF Research Database (Denmark)

    Doerrer, Nancy; Ladics, Gregory; McClain, Scott

    2010-01-01

    established as a standardized assay, survey approaches such as the "-omics" techniques can be considered in a hypothesis-driven analysis of plants, such as determining unintended effects in genetically modified (GM) crops. However, the analysis should include both the GM and control varieties that have...... the same breeding history and exposure to the same environmental conditions. Importantly, the biological relevance and safety significance of changes in "-omic" data are still unknown. Furthermore, the current compositional assessment for evaluating the substantial equivalence of GM crops is robust...... shortcomings identified with "-omics" approaches, a paucity of reference materials, and a lack of focused strategy for their use that currently make them not conducive for the safety assessment of GM crops....

  4. Generation of low-energy muons with laser resonant ionization

    International Nuclear Information System (INIS)

    Matsuda, Y.; Bakule, P.; Iwasaki, M.; Matsuzaki, T.; Miyake, Y.; Ikedo, Y.; Strasser, P.; Shimomura, K.; Makimura, S.; Nagamine, K.

    2006-01-01

    We have constructed a low-energy muSR spectrometer at RIKEN-RAL muon facility in ISIS, the UK. With low-background of pulsed muon beam, and short pulse width from laser resonant ionization method, it is hoped this instrument will open new possibilities for studies of material sciences with muon beam. It is enphasized that this method is well suited to the facility where intense pulsed proton beam is available

  5. Yoshio Nishina father of modern physics in Japan

    CERN Document Server

    Kim, Dong-Won

    2007-01-01

    Yoshio Nishina not only made a great contribution to the emergence of a research network that produced two Nobel prize winners, but he also raised the overall level of physics in Japan. Focusing on his roles as researcher, teacher, and statesman of science, Yoshio Nishina: Father of Modern Physics in Japan analyzes Nishina''s position in and his contributions to the Japanese physics community.After a concise biographical introduction, the book examines Nishina''s family, his early studies, the creation of RIKEN, and the greater Japanese physics community in the early twentieth century. It then focuses on Nishina''s work at the Cavendish Laboratory and at the University of Göttingen as well as his more fruitful research at Niels Bohr''s Institute of Theoretical Physics in Copenhagen. The book also describes the establishment of the Nishina Laboratory at RIKEN, the collaboration between its experimentalists and theoreticians, and the cosmic ray research of its scientists. The last two chapters discuss Nishina'...

  6. Stemcell Information: SKIP000619 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available /ml human basic FGF ... 5% ... Riken Bio Resource Center 理化学研究所バイオリソースセンター Riken Bio Resource Center 理化学...研究所バイオリソースセンター Available Riken Bio Resource Center 理化学研究所バイオリソースセン

  7. Stemcell Information: SKIP000828 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available /100mm dish Primate ES Cell Medium+4ng/ml human basic FGF ... 5% Negative ... RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Available RIKEN BioResource Center 理化学

  8. Stemcell Information: SKIP000636 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available FGF ... 3% Negative ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学研究所バイオリソースセンター RI...KEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Available RIKEN BioResource Center 理化学

  9. Next Generation "Omics" Approaches in the "Fight" against Blood Doping.

    Science.gov (United States)

    Wang, Guan; Karanikolou, Antonia; Verdouka, Ioanna; Friedmann, Theodore; Pitsiladis, Yannis

    2017-01-01

    Despite being prohibited by the World Anti-Doping Agency (WADA), blood manipulations such as the use of recombinant human erythropoietin and blood transfusions are a well-known method used by athletes to enhance performance. Direct detection of illicit blood manipulation has been partially successful due to the short detection window of the substances/methods, sample collection timing, and the use of sophisticated masking strategies. In response, WADA introduced the athlete biological passport (ABP) in 2009, which is an individualised longitudinal monitoring approach that tests primarily haematologic biomarkers of doping in order to identify atypical variability in response(s) in athletes, highlighting a potential doping violation. Although the implementation of the ABP has been an encouraging step forward in the quest for clean/drug-free sport, this detection method has some limitations. To reduce the risk of being detected by the ABP method, athletes are now resorting to microdoses of prohibited blood boosting substances to prevent abnormal fluctuations in haematologic biomarkers, thereby reducing the sensitivity of the ABP detection method. Recent studies from numerous laboratories, including our own, have confirmed the potential of transcriptomic microarrays, which can reveal distinct changes in gene expression after blood manipulations, to enhance the ABP. There is, therefore, an urgent need to intensify research efforts that involve transcriptomics and other state-of-the-art molecular methods, collectively known as "omics", e.g., proteomics (proteins) and metabolomics (metabolites), in order to identify new and even more robust molecular signatures of blood manipulation that can be used in combination with the ABP and, intriguingly, even as a stand-alone test. © 2017 S. Karger AG, Basel.

  10. Biogeochemical typing of paddy field by a data-driven approach revealing sub-systems within a complex environment--a pipeline to filtrate, organize and frame massive dataset from multi-omics analyses.

    Directory of Open Access Journals (Sweden)

    Diogo M O Ogawa

    Full Text Available We propose the technique of biogeochemical typing (BGC typing as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES; and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR spectroscopy and proton nuclear magnetic resonance (1H-NMR all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that

  11. Stemcell Information: SKIP000389 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available +5ng/ml human bFGF ... Riken BioResource Center 理化学研究所バイオリソースセンター Riken BioResource Center 理化学...研究所バイオリソースセンター Available Riken BioResource Center 理化学研究所バイオリソースセンター htt

  12. Stemcell Information: SKIP000618 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available l human basic FGF ... 5% ... Riken Bio Resource Center 理化学研究所バイオリソースセンター Riken Bio Resource Center 理化学...研究所バイオリソースセンター Available Riken Bio Resource Center 理化学研究所バイオリソースセンター

  13. Stemcell Information: SKIP000646 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ing and immunocytochemistry ... No ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学研究所バイオリ...ソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Information Only RIKEN BioResource Center 理化学

  14. Phenotype-gene: 30 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 30 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u3ria224u1029i decreased density of chloroph...b.riken.jp/db/SciNetS_ria224i/cria224u4ria224u15525647i decreased density of chlorophyll http://metadb.riken.jp/db/SciNetS_ria224i/cria224u1ria224u617i AT3G19040

  15. Phenotype-gene: 29 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

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  16. Phenotype-gene: 553 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 553 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u3ria224u1550i non-functional obsolete microgametoph...adb.riken.jp/db/SciNetS_ria224i/cria224u4ria224u11251103i non-functional obsolete microgametophyte http://metadb.riken.jp/db/SciNetS_ria224i/cria224u1ria224u940i AT4G17730

  17. Stemcell Information: SKIP000143 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ... Yes 46XY ... Masayo Takahashi 高橋 政代 Riken Center for Developmental Biology 理研発生再生科学総合研究センター (理研CDB) Ri...ken Center for Developmental Biology 理研発生再生科学総合研究センター (理研CDB) Masayo Takahashi 高橋 政代 Available RIKEN BioReso

  18. Stemcell Information: SKIP000223 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 0.1mM NEAA+0.1mM 2-Mercaptoethanol+5ng/mL human bFGF ... 5% Negative ... RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Available RIKEN BioResource Center 理化学研

  19. Extending Asia Pacific bioinformatics into new realms in the "-omics" era.

    Science.gov (United States)

    Ranganathan, Shoba; Eisenhaber, Frank; Tong, Joo Chuan; Tan, Tin Wee

    2009-12-03

    The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 7-11, 2009 at Biopolis, Singapore. Besides bringing together scientists from the field of bioinformatics in this region, InCoB has actively engaged clinicians and researchers from the area of systems biology, to facilitate greater synergy between these two groups. InCoB2009 followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India), Hong Kong and Taipei (Taiwan), with InCoB2010 scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010. The Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and symposia on Clinical Bioinformatics (CBAS), the Singapore Symposium on Computational Biology (SYMBIO) and training tutorials were scheduled prior to the scientific meeting, and provided ample opportunity for in-depth learning and special interest meetings for educators, clinicians and students. We provide a brief overview of the peer-reviewed bioinformatics manuscripts accepted for publication in this supplement, grouped into thematic areas. In order to facilitate scientific reproducibility and accountability, we have, for the first time, introduced minimum information criteria for our pubilcations, including compliance to a Minimum Information about a Bioinformatics Investigation (MIABi). As the regional research expertise in bioinformatics matures, we have delineated a minimum set of bioinformatics skills required for addressing the computational challenges of the "-omics" era.

  20. Harnessing Integrative Omics to Facilitate Molecular Imaging of the Human Epidermal Growth Factor Receptor Family for Precision Medicine.

    Science.gov (United States)

    Pool, Martin; de Boer, H Rudolf; Hooge, Marjolijn N Lub-de; van Vugt, Marcel A T M; de Vries, Elisabeth G E

    2017-01-01

    Cancer is a growing problem worldwide. The cause of death in cancer patients is often due to treatment-resistant metastatic disease. Many molecularly targeted anticancer drugs have been developed against 'oncogenic driver' pathways. However, these treatments are usually only effective in properly selected patients. Resistance to molecularly targeted drugs through selective pressure on acquired mutations or molecular rewiring can hinder their effectiveness. This review summarizes how molecular imaging techniques can potentially facilitate the optimal implementation of targeted agents. Using the human epidermal growth factor receptor (HER) family as a model in (pre)clinical studies, we illustrate how molecular imaging may be employed to characterize whole body target expression as well as monitor drug effectiveness and the emergence of tumor resistance. We further discuss how an integrative omics discovery platform could guide the selection of 'effect sensors' - new molecular imaging targets - which are dynamic markers that indicate treatment effectiveness or resistance.

  1. Stemcell Information: SKIP000654 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ujioka 藤岡 剛 RIKEN BioResource Center 理化学研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Naka...mura 中村 幸夫 Information Only RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973

  2. Stemcell Information: SKIP000649 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available Fujioka 藤岡 剛 RIKEN BioResource Center 理化学研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Na...kamura 中村 幸夫 Information Only RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 209

  3. Stemcell Information: SKIP000651 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ujioka 藤岡 剛 RIKEN BioResource Center 理化学研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Naka...mura 中村 幸夫 Information Only RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973

  4. Discovery of the "RNA continent" through a contrarian's research strategy.

    Science.gov (United States)

    Hayashizaki, Yoshihide

    2011-01-01

    The International Human Genome Sequencing Consortium completed the decoding of the human genome sequence in 2003. Readers will be aware of the paradigm shift which has occurred since then in the field of life science research. At last, mankind has been able to focus on a complete picture of the full extent of the genome, on which is recorded the basic information that controls all life. Meanwhile, another genome project, centered on Japan and known as the mouse genome encyclopedia project, was progressing with participation from around the world. Led by our research group at RIKEN, it was a full-length cDNA project which aimed to decode the whole RNA (transcriptome) using the mouse as a model. The basic information that controls all life is recorded on the genome, but in order to obtain a complete picture of this extensive information, the decoding of the genome alone is far from sufficient. These two genome projects established that the number of letters in the genome, which is the blueprint of life, is finite, that the number of RNA molecules derived from it is also finite, and that the number of protein molecules derived from the RNA is probably finite too. A massive number of combinations is still involved, but we are now able to understand one section of the network formed by these data. Once an object of study has been understood to be finite, establishing an image of the whole is certain to lead us to an understanding of the whole. Omics is an approach that views the information controlling life as finite and seeks to assemble and analyze it as a whole. Here, I would like to present our transcriptome research while making reference to our unique research strategy.

  5. "Omics" in Human Colostrum and Mature Milk: Looking to Old Data with New Eyes.

    Science.gov (United States)

    Bardanzellu, Flaminia; Fanos, Vassilios; Reali, Alessandra

    2017-08-07

    Human Milk (HM) is the best source for newborn nutrition until at least six months; it exerts anti-inflammatory and anti-infective functions, promotes immune system formation and supports organ development. Breastfeeding could also protect from obesity, diabetes and cardiovascular disease. Furthermore, human colostrum (HC) presents a peculiar role in newborn support as a protective effect against allergic and chronic diseases, in addition to long-term metabolic benefits. In this review, we discuss the recent literature regarding "omics" technologies and growth factors (GF) in HC and the effects of pasteurization on its composition. Our aim was to provide new evidence in terms of transcriptomics, proteomics, metabolomics, and microbiomics, also in relation to maternal metabolic diseases and/or fetal anomalies and to underline the functions of GF. Since HC results are so precious, particularly for the vulnerable pre-terms category, we also discuss the importance of HM pasteurization to ensure donated HC even to neonates whose mothers are unable to provide. To the best of our knowledge, this is the first review analyzing in detail the molecular pattern, microbiota, bioactive factors, and dynamic profile of HC, finding clinical correlations of such mediators with their possible in vivo effects and with the consequent impact on neonatal outcomes.

  6. Stemcell Information: SKIP000278 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available man bFGF ... Negative ... Yes ... Natsumi Shimizu 清水 なつみ RIKEN BioResource Center 理化学研究所バイオリソースセンタ...ー RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Available--Avai...lable--Available RIKEN BioResource Center--Makoto Yazaki(Nagoya City University)--iPS Academia Japan,Inc. 理化学

  7. Integration of Molecular Pathology, Epidemiology, and Social Science for Global Precision Medicine

    Science.gov (United States)

    Nishi, Akihiro; Milner, Danny A; Giovannucci, Edward L.; Nishihara, Reiko; Tan, Andy S.; Kawachi, Ichiro; Ogino, Shuji

    2015-01-01

    Summary The precision medicine concept and the unique disease principle imply that each patient has unique pathogenic processes resulting from heterogeneous cellular genetic and epigenetic alterations, and interactions between cells (including immune cells) and exposures, including dietary, environmental, microbial, and lifestyle factors. As a core method field in population health science and medicine, epidemiology is a growing scientific discipline that can analyze disease risk factors, and develop statistical methodologies to maximize utilization of big data on populations and disease pathology. The evolving transdisciplinary field of molecular pathological epidemiology (MPE) can advance biomedical and health research by linking exposures to molecular pathologic signatures, enhancing causal inference, and identifying potential biomarkers for clinical impact. The MPE approach can be applied to any diseases, although it has been most commonly used in neoplastic diseases (including breast, lung and colorectal cancers) because of availability of various molecular diagnostic tests. However, use of state-of-the-art genomic, epigenomic and other omic technologies and expensive drugs in modern healthcare systems increases racial, ethnic and socioeconomic disparities. To address this, we propose to integrate molecular pathology, epidemiology, and social science. Social epidemiology integrates the latter two fields. The integrative social MPE model can embrace sociology, economics and precision medicine, address global health disparities and inequalities, and elucidate biological effects of social environments, behaviors, and networks. We foresee advancements of molecular medicine, including molecular diagnostics, biomedical imaging, and targeted therapeutics, which should benefit individuals in a global population, by means of an interdisciplinary approach of integrative MPE and social health science. PMID:26636627

  8. Integration of molecular pathology, epidemiology and social science for global precision medicine.

    Science.gov (United States)

    Nishi, Akihiro; Milner, Danny A; Giovannucci, Edward L; Nishihara, Reiko; Tan, Andy S; Kawachi, Ichiro; Ogino, Shuji

    2016-01-01

    The precision medicine concept and the unique disease principle imply that each patient has unique pathogenic processes resulting from heterogeneous cellular genetic and epigenetic alterations and interactions between cells (including immune cells) and exposures, including dietary, environmental, microbial and lifestyle factors. As a core method field in population health science and medicine, epidemiology is a growing scientific discipline that can analyze disease risk factors and develop statistical methodologies to maximize utilization of big data on populations and disease pathology. The evolving transdisciplinary field of molecular pathological epidemiology (MPE) can advance biomedical and health research by linking exposures to molecular pathologic signatures, enhancing causal inference and identifying potential biomarkers for clinical impact. The MPE approach can be applied to any diseases, although it has been most commonly used in neoplastic diseases (including breast, lung and colorectal cancers) because of availability of various molecular diagnostic tests. However, use of state-of-the-art genomic, epigenomic and other omic technologies and expensive drugs in modern healthcare systems increases racial, ethnic and socioeconomic disparities. To address this, we propose to integrate molecular pathology, epidemiology and social science. Social epidemiology integrates the latter two fields. The integrative social MPE model can embrace sociology, economics and precision medicine, address global health disparities and inequalities, and elucidate biological effects of social environments, behaviors and networks. We foresee advancements of molecular medicine, including molecular diagnostics, biomedical imaging and targeted therapeutics, which should benefit individuals in a global population, by means of an interdisciplinary approach of integrative MPE and social health science.

  9. Stemcell Information: SKIP000269 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available and Stroke-like episodes. 疾患特異的iPS細胞株。ミトコンドリア病患者由来。センダイウイルスベクターを用いて4因子(Oct3/4, S...Encephalopathy, Lactic acidosis, and Stroke-like episodes 540000 ... -- -- Japanese Japanese Yes No Disease specific iPS cell...V18+HS-KLF4/TS Delta F, SeV18(HNL)c-MYCQC/TS Delta F ... Yes MEF (X-rays:5000R or MMC) 3-5x10^(5) cells/60mm di...human bFGF ... RikenBRC 理研BRC RikenBRC 理研BRC Available RikenBRC 理研BRC http://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HPS0070&type=1 ...

  10. Stemcell Information: SKIP000661 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available lkaline phosphatase staining and immunocytochemistry ... No ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Information... Only RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973836 10.1111/j.1749-077

  11. Stemcell Information: SKIP000643 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available kaline phosphatase staining and immunocytochemistry ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Information On...ly RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973836 10.1111/j.1749-0774.2

  12. Stemcell Information: SKIP000641 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available Alkaline phosphatase staining and immunocytochemistry ... No ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Informati...on Only RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973836 10.1111/j.1749-0

  13. Stemcell Information: SKIP000220 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 0.1mM 2-Mercaptoethanol+5ng/mL human bFGF ... Yes 46XX(18), 47XX+X(2) ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BRC 理化学...研究所バイオリソースセンター RIKEN BRC 理化学研究所バイオリソースセンター Yukio Nakamura 中村幸夫 Available RIKEN BRC 理化学研究所バイオリ

  14. Stemcell Information: SKIP000657 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available lkaline phosphatase staining and immunocytochemistry ... No ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Information... Only RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973836 10.1111/j.1749-077

  15. Stemcell Information: SKIP000658 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available lkaline phosphatase staining and immunocytochemistry ... No ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Information... Only RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973836 10.1111/j.1749-077

  16. Stemcell Information: SKIP000659 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available lkaline phosphatase staining and immunocytochemistry ... No ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Information... Only RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973836 10.1111/j.1749-077

  17. Stemcell Information: SKIP000642 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available kaline phosphatase staining and immunocytochemistry ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Information On...ly RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973836 10.1111/j.1749-0774.2

  18. Stemcell Information: SKIP000660 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available lkaline phosphatase staining and immunocytochemistry ... No ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Information... Only RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973836 10.1111/j.1749-077

  19. Stemcell Information: SKIP000650 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available lkaline phosphatase staining and immunocytochemistry ... No ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Information... Only RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973836 10.1111/j.1749-077

  20. Stemcell Information: SKIP000656 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available lkaline phosphatase staining and immunocytochemistry ... No ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Information... Only RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973836 10.1111/j.1749-077

  1. Stemcell Information: SKIP000645 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available kaline phosphatase staining and immunocytochemistry ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Information On...ly RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973836 10.1111/j.1749-0774.2

  2. Stemcell Information: SKIP000647 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available staining and immunocytochemistry ... Yes Teratoma formation ... Yes ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Informat...ion Only RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973836 10.1111/j.1749-

  3. Stemcell Information: SKIP000638 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available Alkaline phosphatase staining and immunocytochemistry ... No ... Yes ... Tsuyoshi Fujioka 藤岡 剛 RIKEN BioResource Center 理化学...研究所バイオリソースセンター RIKEN BioResource Center 理化学研究所バイオリソースセンター Yukio Nakamura 中村 幸夫 Informati...on Only RIKEN BioResource Center 理化学研究所バイオリソースセンター ... 20973836 10.1111/j.1749-0

  4. Phenotype-gene: 533 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 533 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u3ria224u1530i low sensitivity toward under influence...nsitivity toward under influence of 1-chloro-2,4-dinitrobenzene http://metadb.riken.jp/db/SciNetS_ria224i/cria224u1ria224u921i AT2G34660 ...Plant Cell Physiol. 49(4):557-69. http://metadb.riken.jp/db/SciNetS_ria224i/cria224u4ria224u18325934i low se

  5. The risk of exposure to Anaplasma phagocytophilum, Borrelia burgdorferi sensu lato, Babesia sp. and co-infections in Ixodes ricinus ticks on the territory of Niepołomice forest (southern Poland).

    Science.gov (United States)

    Asman, Marek; Nowak, Magdalena; Cuber, Piotr; Strzelczyk, Joanna; Szilman, Ewa; Szilman, Piotr; Trapp, Gizela; Siuda, Krzysztof; Solarz, Krzysztof; Wiczkowski, Andrzej

    2013-01-01

    Niepołomice Forest is located about 20 kilometers east of Cracow (Malopolska province, southern Poland). Its natural and touristic values, as well as wide range of hosts occurring within indicate this to be an area of high risk of exposure to Ixodes ricinus and tick-borne diseases it transfers. I. ricinus is a common species in Poland and Europe. Its seasonal activity begins in Poland in the early spring, and ends with late autumn. A total number of 129 specimens of I. ricinus was collected by flagging in Niepołomice Forest. DNA was isolated by ammonia method from 30 randomly-selected individuals. PCR was used to detect tick-borne pathogens with primers specific for Anaplasma phagocytophilum, Borrelia burgdorferi sensu lato and Babesia sp. Molecular studies confirmed the presence of all three pathogens in I. ricinus. A. phagocytophilum was found in 76.7%, Babesia sp., 60%, B. burgdorferi s. l., in 3.3% of studied ticks. A. phagocytophilum co-infection with Babesia sp., was found in 46.7% of the specimens. A co-infection of all three tested pathogens was recorded in one case (3.3%). In Poland the problem of tick-borne diseases is a growing issue, therefore people residing in southern Polish touristic areas should be informed about the prevention and protection against ticks.

  6. RIKEN-JAERI 8-GeV synchrotron radiation project - SPring-8

    International Nuclear Information System (INIS)

    Awaya, Yohko

    1990-01-01

    The plan of an 8-GeV synchrotron radiation facility, which is called SPring-8 (Super Photon Ring-8GeV), had been proposed by Science and Technology Agency (STA) in Japan and it was decided that its construction would be started from April 1990. An atomic physics group in Japan had the first meeting in December 1988 to discuss the future studies of atomic physics and related problems at SPring-8 and plans of research and development (R and D) for them. Their report was published in May 1990. In this report, an outline of SPring-8 is described. Results of the discussions of Japanese working group of atomic physics and the present status of R and D of this group will be presented by M. Kimura in this workshop

  7. H3Africa and the African life sciences ecosystem: building sustainable innovation.

    Science.gov (United States)

    Dandara, Collet; Huzair, Farah; Borda-Rodriguez, Alexander; Chirikure, Shadreck; Okpechi, Ikechi; Warnich, Louise; Masimirembwa, Collen

    2014-12-01

    Interest in genomics research in African populations is experiencing exponential growth. This enthusiasm stems in part from the recognition that the genomic diversity of African populations is a window of opportunity for innovations in postgenomics medicine, ecology, and evolutionary biology. The recently launched H3Africa initiative, for example, captures the energy and momentum of this interest. This interdisciplinary socio-technical analysis highlights the challenges that have beset previous genomics research activities in Africa, and looking ahead, suggests constructive ways H3Africa and similar large scale science efforts could usefully chart a new era of genomics and life sciences research in Africa that is locally productive and globally competitive. As independent African scholars and social scientists, we propose that any serious global omics science effort, including H3Africa, aiming to build genomics research capacity and capability in Africa, needs to fund the establishment of biobanks and the genomic analyses platforms within Africa. Equally they need to prioritize community engagement and bioinformatics capability and the training of African scientists on these platforms. Historically, the financial, technological, and skills imbalance between Africa and developed countries has created exploitative frameworks of collaboration where African researchers have become merely facilitators of Western funded and conceived research agendas involving offshore expatriation of samples. Not surprisingly, very little funding was allocated to infrastructure and human capital development in the past. Moving forward, capacity building should materialize throughout the entire knowledge co-production trajectory: idea generation (e.g., brainstorming workshops for innovative hypotheses development by African scientists), data generation (e.g., genome sequencing), and high-throughput data analysis and contextualization. Additionally, building skills for political science

  8. Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches.

    Science.gov (United States)

    Papadimitriou, Konstantinos; Zoumpopoulou, Georgia; Foligné, Benoit; Alexandraki, Voula; Kazou, Maria; Pot, Bruno; Tsakalidou, Effie

    2015-01-01

    Over the past decades the food industry has been revolutionized toward the production of functional foods due to an increasing awareness of the consumers on the positive role of food in wellbeing and health. By definition probiotic foods must contain live microorganisms in adequate amounts so as to be beneficial for the consumer's health. There are numerous probiotic foods marketed today and many probiotic strains are commercially available. However, the question that arises is how to determine the real probiotic potential of microorganisms. This is becoming increasingly important, as even a superficial search of the relevant literature reveals that the number of proclaimed probiotics is growing fast. While the vast majority of probiotic microorganisms are food-related or commensal bacteria that are often regarded as safe, probiotics from other sources are increasingly being reported raising possible regulatory and safety issues. Potential probiotics are selected after in vitro or in vivo assays by evaluating simple traits such as resistance to the acidic conditions of the stomach or bile resistance, or by assessing their impact on complicated host functions such as immune development, metabolic function or gut-brain interaction. While final human clinical trials are considered mandatory for communicating health benefits, rather few strains with positive studies have been able to convince legal authorities with these health claims. Consequently, concern has been raised about the validity of the workflows currently used to characterize probiotics. In this review we will present an overview of the most common assays employed in screening for probiotics, highlighting the potential strengths and limitations of these approaches. Furthermore, we will focus on how the advent of omics technologies has reshaped our understanding of the biology of probiotics, allowing the exploration of novel routes for screening and studying such microorganisms.

  9. Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches

    Directory of Open Access Journals (Sweden)

    Konstantinos ePapadimitriou

    2015-02-01

    Full Text Available Over the past decades the food industry has been revolutionized towards the production of functional foods due to an increasing awareness of the consumers on the positive role of food in wellbeing and health. By definition probiotic foods must contain live microorganisms in adequate amounts so as to be beneficial for the consumer’s health. There are numerous probiotic foods marketed today and many probiotic strains are commercially available. However, the question that arises is how to determine the real probiotic potential of microorganisms. This is becoming increasingly important, as even a superficial search of the relevant literature reveals that the number of proclaimed probiotics is growing fast. While the vast majority of probiotic microorganisms are food-related or commensal bacteria that are often regarded as safe, probiotics from other sources are increasingly being reported raising possible regulatory and safety issues. Potential probiotics are selected after in vitro or in vivo assays by evaluating simple traits such as resistance to the acidic conditions of the stomach or bile resistance, or by assessing their impact on complicated host functions such as immune development, metabolic function or gut-brain interaction. While final human clinical trials are considered mandatory for communicating health benefits, rather few strains with positive studies have been able to convince legal authorities with these health claims. Consequently, concern has been raised about the validity of the workflows currently used to characterize probiotics. In this review we will present an overview of the most common assays employed in screening for probiotics, highlighting the potential strengths and limitations of these approaches. Furthermore, we will focus on how the advent of omics technologies has reshaped our understanding of the biology of probiotics, allowing the exploration of novel routes for screening and studying such microorganisms.

  10. Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches

    Science.gov (United States)

    Papadimitriou, Konstantinos; Zoumpopoulou, Georgia; Foligné, Benoit; Alexandraki, Voula; Kazou, Maria; Pot, Bruno; Tsakalidou, Effie

    2015-01-01

    Over the past decades the food industry has been revolutionized toward the production of functional foods due to an increasing awareness of the consumers on the positive role of food in wellbeing and health. By definition probiotic foods must contain live microorganisms in adequate amounts so as to be beneficial for the consumer’s health. There are numerous probiotic foods marketed today and many probiotic strains are commercially available. However, the question that arises is how to determine the real probiotic potential of microorganisms. This is becoming increasingly important, as even a superficial search of the relevant literature reveals that the number of proclaimed probiotics is growing fast. While the vast majority of probiotic microorganisms are food-related or commensal bacteria that are often regarded as safe, probiotics from other sources are increasingly being reported raising possible regulatory and safety issues. Potential probiotics are selected after in vitro or in vivo assays by evaluating simple traits such as resistance to the acidic conditions of the stomach or bile resistance, or by assessing their impact on complicated host functions such as immune development, metabolic function or gut–brain interaction. While final human clinical trials are considered mandatory for communicating health benefits, rather few strains with positive studies have been able to convince legal authorities with these health claims. Consequently, concern has been raised about the validity of the workflows currently used to characterize probiotics. In this review we will present an overview of the most common assays employed in screening for probiotics, highlighting the potential strengths and limitations of these approaches. Furthermore, we will focus on how the advent of omics technologies has reshaped our understanding of the biology of probiotics, allowing the exploration of novel routes for screening and studying such microorganisms. PMID:25741323

  11. BROOKHAVEN: Japanese collaboration

    International Nuclear Information System (INIS)

    Thieberger, Peter

    1995-01-01

    Full text: The Japanese RIKEN Laboratory is contributing $20 million to help construct the RHIC Relativistic Heavy Ion Collider now being built at Brookhaven and due to be completed in 1999. In return, RIKEN will participate in research at RHIC. RHIC is being built to collide beams of heavy ions at energies of about 100 GeV per nucleon to explore hot and dense states of nuclear matter, with the ultimate aim of finding the quark-gluon plasma, the medium which existed in the fiery aftermath of the Big Bang before subsequently 'freezing' into nucleons. However another long-time Brookhaven speciality is handling beams of polarized (spin-oriented) protons in the 30 GeV AGS Alternating Gradient Synchrotron, which will act as the injector for RHIC. With the involvement of RIKEN, the RHIC programme now expands to cover polarized protons. Half of the RIKEN support will be used to build and install the special hardware needed to handle the polarized beams in RHIC. This includes 'Siberian Snakes' to negotiate depolarizing resonances which would otherwise mar beam acceleration (September 1994, page 27). The remaining RIKEN funding will go towards additional equipment for the PHENIX detector (May 1992, page 10) to enable it to cover spin physics. This equipment includes a second muon arm, with a magnet and tracking chamber. A multidisciplinary laboratory, RIKEN - Rikagaku Kenkyusho, or the Institute of Physical and Chemical Research - near Tokyo is currently the scene of construction of an 8 GeV synchrotron X-ray source

  12. Rediscovering medicinal plants' potential with OMICS: microsatellite survey in expressed sequence tags of eleven traditional plants with potent antidiabetic properties.

    Science.gov (United States)

    Sahu, Jagajjit; Sen, Priyabrata; Choudhury, Manabendra Dutta; Dehury, Budheswar; Barooah, Madhumita; Modi, Mahendra Kumar; Talukdar, Anupam Das

    2014-05-01

    Herbal medicines and traditionally used medicinal plants present an untapped potential for novel molecular target discovery using systems science and OMICS biotechnology driven strategies. Since up to 40% of the world's poor people have no access to government health services, traditional and folk medicines are often the only therapeutics available to them. In this vein, North East (NE) India is recognized for its rich bioresources. As part of the Indo-Burma hotspot, it is regarded as an epicenter of biodiversity for several plants having myriad traditional uses, including medicinal use. However, the improvement of these valuable bioresources through molecular breeding strategies, for example, using genic microsatellites or Simple Sequence Repeats (SSRs) or Expressed Sequence Tags (ESTs)-derived SSRs has not been fully utilized in large scale to date. In this study, we identified a total of 47,700 microsatellites from 109,609 ESTs of 11 medicinal plants (pineapple, papaya, noyontara, bitter orange, bermuda brass, ratalu, barbados nut, mango, mulberry, lotus, and guduchi) having proven antidiabetic properties. A total of 58,159 primer pairs were designed for the non-redundant 8060 SSR-positive ESTs and putative functions were assigned to 4483 unique contigs. Among the identified microsatellites, excluding mononucleotide repeats, di-/trinucleotides are predominant, among which repeat motifs of AG/CT and AAG/CTT were most abundant. Similarity search of SSR containing ESTs and antidiabetic gene sequences revealed 11 microsatellites linked to antidiabetic genes in five plants. GO term enrichment analysis revealed a total of 80 enriched GO terms widely distributed in 53 biological processes, 17 molecular functions, and 10 cellular components associated with the 11 markers. The present study therefore provides concrete insights into the frequency and distribution of SSRs in important medicinal resources. The microsatellite markers reported here markedly add to the genetic

  13. Phenotype abnormality: 384 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available of stomatal complex in environment of light regimen in environment of light regimen http://metadb.riken.jp/d... 384 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u1ria224u889i increased size

  14. Phenotype abnormality: 415 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available nment of soil environment in environment of soil environment http://metadb.riken.jp... 415 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u1ria224u919i lethal in organ named seedling in enviro

  15. A semantic web framework to integrate cancer omics data with biological knowledge.

    Science.gov (United States)

    Holford, Matthew E; McCusker, James P; Cheung, Kei-Hoi; Krauthammer, Michael

    2012-01-25

    The RDF triple provides a simple linguistic means of describing limitless types of information. Triples can be flexibly combined into a unified data source we call a semantic model. Semantic models open new possibilities for the integration of variegated biological data. We use Semantic Web technology to explicate high throughput clinical data in the context of fundamental biological knowledge. We have extended Corvus, a data warehouse which provides a uniform interface to various forms of Omics data, by providing a SPARQL endpoint. With the querying and reasoning tools made possible by the Semantic Web, we were able to explore quantitative semantic models retrieved from Corvus in the light of systematic biological knowledge. For this paper, we merged semantic models containing genomic, transcriptomic and epigenomic data from melanoma samples with two semantic models of functional data - one containing Gene Ontology (GO) data, the other, regulatory networks constructed from transcription factor binding information. These two semantic models were created in an ad hoc manner but support a common interface for integration with the quantitative semantic models. Such combined semantic models allow us to pose significant translational medicine questions. Here, we study the interplay between a cell's molecular state and its response to anti-cancer therapy by exploring the resistance of cancer cells to Decitabine, a demethylating agent. We were able to generate a testable hypothesis to explain how Decitabine fights cancer - namely, that it targets apoptosis-related gene promoters predominantly in Decitabine-sensitive cell lines, thus conveying its cytotoxic effect by activating the apoptosis pathway. Our research provides a framework whereby similar hypotheses can be developed easily.

  16. Crop improvement using life cycle datasets acquired under field conditions.

    Science.gov (United States)

    Mochida, Keiichi; Saisho, Daisuke; Hirayama, Takashi

    2015-01-01

    Crops are exposed to various environmental stresses in the field throughout their life cycle. Modern plant science has provided remarkable insights into the molecular networks of plant stress responses in laboratory conditions, but the responses of different crops to environmental stresses in the field need to be elucidated. Recent advances in omics analytical techniques and information technology have enabled us to integrate data from a spectrum of physiological metrics of field crops. The interdisciplinary efforts of plant science and data science enable us to explore factors that affect crop productivity and identify stress tolerance-related genes and alleles. Here, we describe recent advances in technologies that are key components for data driven crop design, such as population genomics, chronological omics analyses, and computer-aided molecular network prediction. Integration of the outcomes from these technologies will accelerate our understanding of crop phenology under practical field situations and identify key characteristics to represent crop stress status. These elements would help us to genetically engineer "designed crops" to prevent yield shortfalls because of environmental fluctuations due to future climate change.

  17. Crop improvement using life cycle datasets acquired under field conditions

    Directory of Open Access Journals (Sweden)

    Keiichi eMochida

    2015-09-01

    Full Text Available Crops are exposed to various environmental stresses in the field throughout their life cycle. Modern plant science has provided remarkable insights into the molecular networks of plant stress responses in laboratory conditions, but the responses of different crops to environmental stresses in the field need to be elucidated. Recent advances in omics analytical techniques and information technology have enabled us to integrate data from a spectrum of physiological metrics of field crops. The interdisciplinary efforts of plant science and data science enable us to explore factors that affect crop productivity and identify stress tolerance-related genes and alleles. Here, we describe recent advances in technologies that are key components for data driven crop design, such as population genomics, chronological omics analyses, and computer-aided molecular network prediction. Integration of the outcomes from these technologies will accelerate our understanding of crop phenology under practical field situations and identify key characteristics to represent crop stress status. These elements would help us to genetically engineer designed crops to prevent yield shortfalls because of environmental fluctuations due to future climate change.

  18. Toxicogenomics in Environmental Science.

    Science.gov (United States)

    Brinke, Alexandra; Buchinger, Sebastian

    This chapter reviews the current knowledge and recent progress in the field of environmental, aquatic ecotoxicogenomics with a focus on transcriptomic methods. In ecotoxicogenomics the omics technologies are applied for the detection and assessment of adverse effects in the environment, and thus are to be distinguished from omics used in human toxicology [Snape et al., Aquat Toxicol 67:143-154, 2004]. Transcriptomic methods in ecotoxicology are applied to gain a mechanistic understanding of toxic effects on organisms or populations, and thus aim to bridge the gap between cause and effect. A worthwhile effect-based interpretation of stressor induced changes on the transcriptome is based on the principle of phenotypic-anchoring [Paules, Environ Health Perspect 111:A338-A339, 2003]. Thereby, changes on the transcriptomic level can only be identified as effects if they are clearly linked to a specific stressor-induced effect on the macroscopic level. By integrating those macroscopic and transcriptomic effects, conclusions on the effect-inducing type of the stressor can be drawn. Stressor-specific effects on the transcriptomic level can be identified as stressor-specific induced pathways, transcriptomic patterns, or stressors-specific genetic biomarkers. In this chapter, examples of the combined application of macroscopic and transcriptional effects for the identification of environmental stressors, such as aquatic pollutants, are given and discussed. By means of these examples, challenges on the way to a standardized application of transcriptomics in ecotoxicology are discussed. This is also done against the background of the application of transcriptomic methods in environmental regulation such as the EU regulation Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH).

  19. Big Data Transforms Discovery-Utilization Therapeutics Continuum.

    Science.gov (United States)

    Waldman, S A; Terzic, A

    2016-03-01

    Enabling omic technologies adopt a holistic view to produce unprecedented insights into the molecular underpinnings of health and disease, in part, by generating massive high-dimensional biological data. Leveraging these systems-level insights as an engine driving the healthcare evolution is maximized through integration with medical, demographic, and environmental datasets from individuals to populations. Big data analytics has accordingly emerged to add value to the technical aspects of storage, transfer, and analysis required for merging vast arrays of omic-, clinical-, and eco-datasets. In turn, this new field at the interface of biology, medicine, and information science is systematically transforming modern therapeutics across discovery, development, regulation, and utilization. © 2015 ASCPT.

  20. The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments.

    Science.gov (United States)

    Kodama, Yuichi; Mashima, Jun; Kaminuma, Eli; Gojobori, Takashi; Ogasawara, Osamu; Takagi, Toshihisa; Okubo, Kousaku; Nakamura, Yasukazu

    2012-01-01

    The DNA Data Bank of Japan (DDBJ; http://www.ddbj.nig.ac.jp) maintains and provides archival, retrieval and analytical resources for biological information. The central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: the 'DDBJ Omics Archive' (DOR; http://trace.ddbj.nig.ac.jp/dor) and BioProject (http://trace.ddbj.nig.ac.jp/bioproject). DOR is an archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. In this article, we describe major changes and improvements introduced to the DDBJ services, and the launch of two new resources: DOR and BioProject.

  1. BDML Metadata: 386 [SSBD[Archive

    Lifescience Database Archive (English)

    Full Text Available fused reconstruction of early Drosophila wild-type development D. melanogaster nuclear positions drosophila...bic.riken.jp/data/bdml/DM_PJK/drosophila_fused.bdml0.15.xml http://ssbd.qbic.riken.jp/search/d5093809-afbb-4f54-afd2-96bad998ac7e/ ...

  2. Astrophysics at RIA (ARIA) Working Group

    International Nuclear Information System (INIS)

    Smith, Michael S.; Schatz, Hendrik; Timmes, Frank X.; Wiescher, Michael; Greife, Uwe

    2006-01-01

    The Astrophysics at RIA (ARIA) Working Group has been established to develop and promote the nuclear astrophysics research anticipated at the Rare Isotope Accelerator (RIA). RIA is a proposed next-generation nuclear science facility in the U.S. that will enable significant progress in studies of core collapse supernovae, thermonuclear supernovae, X-ray bursts, novae, and other astrophysical sites. Many of the topics addressed by the Working Group are relevant for the RIKEN RI Beam Factory, the planned GSI-Fair facility, and other advanced radioactive beam facilities

  3. A Multi-omics Approach to Understand the Microbial Transformation of Lignocellulosic Materials in the Digestive System of the Wood-Feeding Beetle Odontotaenius disjunctus

    Science.gov (United States)

    Ceja Navarro, J. A.; Karaoz, U.; White, R. A., III; Lipton, M. S.; Adkins, J.; Mayali, X.; Blackwell, M.; Pett-Ridge, J.; Brodie, E.; Hao, Z.

    2015-12-01

    Odontotaenius disjuctus is a wood feeding beetle that processes large amounts of hardwoods and plays an important role in forest carbon cycling. In its gut, plant material is transformed into simple molecules by sequential processing during passage through the insect's digestive system. In this study, we used multiple 'omics approaches to analyze the distribution of microbial communities and their specific functions in lignocellulose deconstruction within the insect's gut. Fosmid clones were selected and sequenced from a pool of clones based on their expression of plant polymer degrading enzymes, allowing the identification of a wide range of carbohydrate degrading enzymes. Comparison of metagenomes of all gut regions demonstrated the distribution of genes across the beetle gut. Cellulose, starch, and xylan degradation genes were particularly abundant in the midgut and posterior hindgut. Genes involved in hydrogenotrophic production of methane and nitrogenases were more abundant in the anterior hindgut. Assembled contigs were binned into 127 putative genomes representing Bacteria, Archaea, Fungi and Nematodes. Eleven complete genomes were reconstructed allowing to identify linked functions/traits, including organisms with cellulosomes, and a combined potential for cellulose, xylan and starch hydrolysis and nitrogen fixation. A metaproteomic study was conducted to test the expression of the pathways identified in the metagenomic study. Preliminary analyses suggest enrichment of pathways related to hemicellulosic degradation. A complete xylan degradation pathway was reconstructed and GC-MS/MS based metabolomics identified xylobiose and xylose as major metabolite pools. To relate microbial identify to function in the beetle gut, Chip-SIP isotope tracing was conducted with RNA extracted from beetles fed 13C-cellulose. Multiple 13C enriched bacterial groups were detected, mainly in the midgut. Our multi-omics approach has allowed us to characterize the contribution of

  4. The health effects of bioactive plant components in food: Results and opinions of the EU COST 926 action

    NARCIS (Netherlands)

    Dokkum, W. van; Frølich, W.; Saltmarsh, M.; Gee, J.

    2008-01-01

    COST (European Cooperation in the field of Scientific and Technical Research) Action 926 is a networking partnership funded by the European Union through the European Science Foundation. Scientists involved have evaluated whether or not the new 'omic' technologies can offer a means of obtaining the

  5. Gestures to intuitively control large displays : 7th International Gesture Workshop, GW 2007, Lisbon, Portugal, May 23-25, 2007 : revised selected papers

    NARCIS (Netherlands)

    Fikkert, W.; van der Vet, P.; Rauwerda, H.; Breit, T.; Nijholt, A.; Sales Dias, M.; Gibet, S.; Wanderley, M.M.; Bastos, R.

    2009-01-01

    Large displays are highly suited to support discussions in empirical science. Such displays can display project results on a large digital surface to feed the discussion. This paper describes our approach to closely involve multidisciplinary omics scientists in the design of an intuitive display

  6. Nanotechnology R and D Policy of Japan and Nanotechnology Support Project

    International Nuclear Information System (INIS)

    Kishi, Teruo

    2004-01-01

    In the 2nd Science and Technology Basic Plan (2001-2005), the area of nanotechnology and materials is designated one of the four prioritized areas in funding. Following this plan, Ministry of Education, Culture, Sports, Science and Technology (MEXT) and Ministry of Economy, Trade and Industries (METI), the main funding ministries, and their organizations, Japan Society for the Promotion of Science (JSPS), Japan Science and Technology Agency (JST), National Institute for Materials Science (NIMS), RIKEN, New Energy and Industrial Technology Organization (NEDO), and National Institute of Advanced Industrial Science and Technology (AIST) promotes their research programs. Besides, in order to promote interdisciplinary, interorganizational, and international collaboration of researchers, Nanotechnology Support Project (NSP) was started by MEXT in 2002. The project has two missions: informational support and common use facility support. Nanotechnology Researchers Network Center of Japan is responsible for informational support, and 14 universities and national research institutes are responsible for common use facility support

  7. Phenotype-gene: 424 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 424 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u3ria224u1421i increased number of axillary inflore...scence bud in organ named inflorescence for AT5G15230 Roxrud Ingrid et al. 2007 Mar. P...ed number of axillary inflorescence bud in organ named inflorescence http://metadb.riken.jp/db/SciNetS_ria224i/cria224u1ria224u839i AT5G15230 ...lant Cell Physiol. 48(3):471-83. http://metadb.riken.jp/db/SciNetS_ria224i/cria224u4ria224u17284469i increas

  8. Phenotype-gene: 774 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ology in organ named obsolete microgametophyte for AT5G11110 Suzuki Toshiya et al. 2008 Oct. Plant Cell Ph... 774 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u3ria224u950i abnormal for trait of morph...ysiol. 49(10):1465-77. http://metadb.riken.jp/db/SciNetS_ria224i/cria224u4ria224u18779216i abnormal for trait of morph...ology in organ named obsolete microgametophyte http://metadb.riken.jp/db/SciNetS_ria224i/cria224u1ria224u567i AT5G11110

  9. Phenotype-gene: 529 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available onment of soil environment for AT3G62910 Motohashi Reiko et al. 2007 Jul. Plant Mol...nt of soil environment http://metadb.riken.jp/db/SciNetS_ria224i/cria224u1ria224u919i AT3G62910 .... Biol. 64(5):481-97. http://metadb.riken.jp/db/SciNetS_ria224i/cria224u4ria224u17450416i lethal in organ named seedling in environme... 529 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u3ria224u1526i lethal in organ named seedling in envir

  10. The bacterial rhizobiome of hyperaccumulators: future perspectives based on omics analysis and advanced microscopy

    Directory of Open Access Journals (Sweden)

    Giovanna eVisioli

    2015-01-01

    Full Text Available Hyperaccumulators are plants that can extract heavy metal ions from the soil and translocate those ions to the shoots, where they are sequestered and detoxified. Hyperaccumulation depends not only on the availability of mobilized metal ions in the soil, but also on the enhanced activity of metal transporters and metal chelators which may be provided by the plant or its associated microbes. The rhizobiome is captured by plant root exudates from the complex microbial community in the soil, and may colonize the root surface or infiltrate the root cortex. This community can increase the root surface area by inducing hairy root proliferation. It may also increase the solubility of metals in the rhizosphere and promote the uptake of soluble metals by the plant. The bacterial rhizobiome, a subset of specialized microorganisms that colonize the plant rhizosphere and endosphere, makes an important contribution to the hyperaccumulator phenotype. In this review, we discuss classic and more recent tools that are used to study the interactions between hyperaccumulators and the bacterial rhizobiome, and consider future perspectives based on the use of omics analysis and microscopy to study plant metabolism in the context of metal accumulation. Recent data suggest that metal-resistant bacteria isolated from the hyperaccumulator rhizosphere and endosphere could be useful in applications such as phytoextraction and phytoremediation, although more research is required to determine whether such properties can be transferred successfully to non-accumulator species.

  11. An integrative 'omics' solution to the detection of recombinant human erythropoietin and blood doping.

    Science.gov (United States)

    Pitsiladis, Yannis P; Durussel, Jérôme; Rabin, Olivier

    2014-05-01

    Administration of recombinant human erythropoietin (rHumanEPO) improves sporting performance and hence is frequently subject to abuse by athletes, although rHumanEPO is prohibited by the WADA. Approaches to detect rHumanEPO doping have improved significantly in recent years but remain imperfect. A new transcriptomic-based longitudinal screening approach is being developed that has the potential to improve the analytical performance of current detection methods. In particular, studies are being funded by WADA to identify a 'molecular signature' of rHumanEPO doping and preliminary results are promising. In the first systematic study to be conducted, the expression of hundreds of genes were found to be altered by rHumanEPO with numerous gene transcripts being differentially expressed after the first injection and further transcripts profoundly upregulated during and subsequently downregulated up to 4 weeks postadministration of the drug; with the same transcriptomic pattern observed in all participants. The identification of a blood 'molecular signature' of rHumanEPO administration is the strongest evidence to date that gene biomarkers have the potential to substantially improve the analytical performance of current antidoping methods such as the Athlete Biological Passport for rHumanEPO detection. Given the early promise of transcriptomics, research using an 'omics'-based approach involving genomics, transcriptomics, proteomics and metabolomics should be intensified in order to achieve improved detection of rHumanEPO and other doping substances and methods difficult to detect such a recombinant human growth hormone and blood transfusions.

  12. Stemcell Information: SKIP000108 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ... -- -- ... Yes No intractable disease-specific iPSC 難病性疾患克服事業iPS細胞バンク human ES-like -- Sendai virus S... Not Available RikenBRC 理研BRC http://www.brc.riken.jp/lab/cell/english/patient_specific_ips.shtml ...

  13. Stemcell Information: SKIP000128 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ... -- -- ... Yes No intractable disease-specific iPSC 難病性疾患克服事業iPS細胞バンク human ES-like -- Sendai virus S... Not Available RikenBRC 理研BRC http://www.brc.riken.jp/lab/cell/english/patient_specific_ips.shtml ...

  14. BDML Metadata: 385 [SSBD[Archive

    Lifescience Database Archive (English)

    Full Text Available fused reconstruction of early Drosophila wild-type development D. melanogaster nuclear positions drosophila...bic.riken.jp/data/bdml/DM_PJK/drosophila_fused.bdml0.18.zip http://ssbd.qbic.riken.jp/search/10180487-6e38-4234-ba5b-b162e0bf0d39/ ...

  15. Why Are Omics Technologies Important to Understanding the Role of Nutrition in Inflammatory Bowel Diseases?

    Directory of Open Access Journals (Sweden)

    Lynnette R. Ferguson

    2016-10-01

    Full Text Available For many years, there has been confusion about the role that nutrition plays in inflammatory bowel diseases (IBD. It is apparent that good dietary advice for one individual may prove inappropriate for another. As with many diseases, genome-wide association studies across large collaborative groups have been important in revealing the role of genetics in IBD, with more than 200 genes associated with susceptibility to the disease. These associations provide clues to explain the differences in nutrient requirements among individuals. In addition to genes directly involved in the control of inflammation, a number of the associated genes play roles in modulating the gut microbiota. Cell line models enable the generation of hypotheses as to how various bioactive dietary components might be especially beneficial for certain genetic groups. Animal models are necessary to mimic aspects of the complex aetiology of IBD, and provide an important link between tissue culture studies and human trials. Once we are sufficiently confident of our hypotheses, we can then take modified diets to an IBD population that is stratified according to genotype. Studies in IBD patients fed a Mediterranean-style diet have been important in validating our hypotheses and as a proof-of-principle for the application of these sensitive omics technologies to aiding in the control of IBD symptoms.

  16. Integrative analysis of multiple diverse omics datasets by sparse group multitask regression

    Directory of Open Access Journals (Sweden)

    Dongdong eLin

    2014-10-01

    Full Text Available A variety of high throughput genome-wide assays enable the exploration of genetic risk factors underlying complex traits. Although these studies have remarkable impact on identifying susceptible biomarkers, they suffer from issues such as limited sample size and low reproducibility. Combining individual studies of different genetic levels/platforms has the promise to improve the power and consistency of biomarker identification. In this paper, we propose a novel integrative method, namely sparse group multitask regression, for integrating diverse omics datasets, platforms and populations to identify risk genes/factors of complex diseases. This method combines multitask learning with sparse group regularization, which will: 1 treat the biomarker identification in each single study as a task and then combine them by multitask learning; 2 group variables from all studies for identifying significant genes; 3 enforce sparse constraint on groups of variables to overcome the ‘small sample, but large variables’ problem. We introduce two sparse group penalties: sparse group lasso and sparse group ridge in our multitask model, and provide an effective algorithm for each model. In addition, we propose a significance test for the identification of potential risk genes. Two simulation studies are performed to evaluate the performance of our integrative method by comparing it with conventional meta-analysis method. The results show that our sparse group multitask method outperforms meta-analysis method significantly. In an application to our osteoporosis studies, 7 genes are identified as significant genes by our method and are found to have significant effects in other three independent studies for validation. The most significant gene SOD2 has been identified in our previous osteoporosis study involving the same expression dataset. Several other genes such as TREML2, HTR1E and GLO1 are shown to be novel susceptible genes for osteoporosis, as confirmed

  17. Arsenic and Environmental Health: State of the Science and ...

    Science.gov (United States)

    Background: Exposure to inorganic and organic arsenic compounds is a major public health problem that affects hundreds of millions of people worldwide. Exposure to arsenic is associated with cancer and noncancer effects in nearly every organ in the body, and evidence is mounting for health effects at lower levels of arsenic exposure than previously thought. Building from a tremendous knowledge base with > 1,000 scientific papers published annually with “arsenic” in the title, the question becomes, what questions would best drive future research directions? Objectives: The objective is to discuss emerging issues in arsenic research and identify data gaps across disciplines. Methods: The National Institutes of Health’s National Institute of Environmental Health Sciences Superfund Research Program convened a workshop to identify emerging issues and research needs to address the multi-faceted challenges related to arsenic and environmental health. This review summarizes information captured during the workshop. Discussion: More information about aggregate exposure to arsenic is needed, including the amount and forms of arsenic found in foods. New strategies for mitigating arsenic exposures and related health effects range from engineered filtering systems to phytogenetics and nutritional interventions. Furthermore, integration of omics data with mechanistic and epidemiological data is a key step toward the goal of linking biomarkers of exposure and suscepti

  18. Phenotype-gene: 494 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 494 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u3ria224u1491i inpaired stomatal movement... http://metadb.riken.jp/db/SciNetS_ria224i/cria224u4ria224u12773379i inpaired stomatal movement in presence

  19. Phenotype-gene: 753 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 753 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u3ria224u929i abnormal for trait of behavior...tadb.riken.jp/db/SciNetS_ria224i/cria224u4ria224u12694594i abnormal for trait of behavior

  20. Phenotype-gene: 475 [Arabidopsis Phenome Database[Archive

    Lifescience Database Archive (English)

    Full Text Available 475 http://metadb.riken.jp/db/SciNetS_ria224i/cria224u3ria224u1472i increased sensitivity under influence...//metadb.riken.jp/db/SciNetS_ria224i/cria224u4ria224u17355438i increased sensitivity under influence of lead