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.

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

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

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

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.

Profiling microbial lignocellulose degradation and utilization by emergent omics technologies.

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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.

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

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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.

Somatic Embryogenesis in Coffee: The Evolution of Biotechnology and the Integration of Omics Technologies Offer Great Opportunities.

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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.

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.

-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.

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.

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.

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.

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.

-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

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.

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

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.

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.

[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.

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.

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.

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.

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

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...

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

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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.

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

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.

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

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.

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.

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.

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.

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

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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.

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.

"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.

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

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

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?

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.

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.

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.

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

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.

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...

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

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.

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.

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.

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.

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.

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.

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.

Application of Omics Technologies in the System of Sports Training

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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.

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.

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

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.

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

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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.

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

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Demura Taku

2006-03-01

Full Text Available Abstract Background In order to understand microarray data reasonably in the context of other existing biological knowledge, it is necessary to conduct a thorough examination of the data utilizing every aspect of available omic knowledge libraries. So far, a number of bioinformatics tools have been developed. However, each of them is restricted to deal with one type of omic knowledge, e.g., pathways, interactions or gene ontology. Now that the varieties of omic knowledge are expanding, analysis tools need a way to deal with any type of omic knowledge. Hence, we have designed the Omic Space Markup Language (OSML that can represent a wide range of omic knowledge, and also, we have developed a tool named GSCope3, which can statistically analyze microarray data in comparison with the OSML-formatted omic knowledge data. Results In order to test the applicability of OSML to represent a variety of omic knowledge specifically useful for analysis of Arabidopsis thaliana microarray data, we have constructed a Biological Knowledge Library (BiKLi by converting eight different types of omic knowledge into OSML-formatted datasets. We applied GSCope3 and BiKLi to previously reported A. thaliana microarray data, so as to extract any additional insights from the data. As a result, we have discovered a new insight that lignin formation resists drought stress and activates transcription of many water channel genes to oppose drought stress; and most of the 20S proteasome subunit genes show similar expression profiles under drought stress. In addition to this novel discovery, similar findings previously reported were also quickly confirmed using GSCope3 and BiKLi. Conclusion GSCope3 can statistically analyze microarray data in the context of any OSML-represented omic knowledge. OSML is not restricted to a specific data type structure, but it can represent a wide range of omic knowledge. It allows us to convert new types of omic knowledge into datasets that can be

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

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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.

Integration of electronic nose technology with spirometry: validation of a new approach for exhaled breath analysis

NARCIS (Netherlands)

de Vries, R.; Brinkman, P.; van der Schee, M. P.; Fens, N.; Dijkers, E.; Bootsma, S. K.; de Jongh, F. H. C.; Sterk, P. J.

2015-01-01

New 'omics'-technologies have the potential to better define airway disease in terms of pathophysiological and clinical phenotyping. The integration of electronic nose (eNose) technology with existing diagnostic tests, such as routine spirometry, can bring this technology to 'point-of-care'. We

Omics Data Complementarity Underlines Functional Cross-Communication in Yeast

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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.

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.

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.

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.

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

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

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

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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.

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

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

Comprehensive insights into microcystin-LR effects on hepatic lipid metabolism using cross-omics technologies

International Nuclear Information System (INIS)

Zhang, Zongyao; Zhang, Xu-Xiang; Wu, Bing; Yin, Jinbao; Yu, Yunjiang; Yang, Liuyan

2016-01-01

Highlights: • Use of cross-omics technologies to evaluate toxic effects of microcystin-LR. • Disturbance of hepatic lipid metabolism by oral exposure to microcystin-LR. • Crucial roles of gut microbial community shift in the metabolic disturbance induced by microcystin-LR. - Abstract: Microcystin-LR (MC-LR) can induce hepatic tissue damages and molecular toxicities, but its effects on lipid metabolism remain unknown. This study investigated the effects of MC-LR exposure on mice lipid metabolism and uncovered the underlying mechanism through metabonomic, transcriptomic and metagenomic analyses after administration of mice with MC-LR by gavage for 28 d. Increased liver weight and abdominal fat weight, and evident hepatic lipid vacuoles accumulation were observed in the mice fed with 0.2 mg/kg/d MC-LR. Serum nuclear magnetic resonance analysis showed that MC-LR treatment altered the levels of serum metabolites including triglyceride, unsaturated fatty acid (UFA) and very low density lipoprotein. Digital Gene Expression technology was used to reveal differential expression of hepatic transcriptomes, demonstrating that MC-LR treatment disturbed hepatic UFA biosynthesis and activated peroxisome proliferator-activated receptor (PPAR) signaling pathways via Pparγ, Fabp1 and Fabp2 over-expression. Metagenomic analyses of gut microbiota revealed that MC-LR exposure also increased abundant ratio of Firmicutes vs. Bacteroidetes in gut and altered biosynthetic pathways of various microbial metabolic and pro-inflammatory molecules. In conclusion, oral MC-LR exposure can induce hepatic lipid metabolism disorder mediated by UFA biosynthesis and PPAR activation, and gut microbial community shift may play an important role in the metabolic disturbance.

Comprehensive insights into microcystin-LR effects on hepatic lipid metabolism using cross-omics technologies

Energy Technology Data Exchange (ETDEWEB)

Zhang, Zongyao [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023 (China); Center for Environmental Health Research, South China Institute of Environmental Sciences, The Ministry of Environmental Protection of PRC, Guangzhou 510655 (China); Zhang, Xu-Xiang, E-mail: zhangxx@nju.edu.cn [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023 (China); Wu, Bing; Yin, Jinbao [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023 (China); Yu, Yunjiang [Center for Environmental Health Research, South China Institute of Environmental Sciences, The Ministry of Environmental Protection of PRC, Guangzhou 510655 (China); Yang, Liuyan, E-mail: yangly@nju.edu.cn [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023 (China)

2016-09-05

Highlights: • Use of cross-omics technologies to evaluate toxic effects of microcystin-LR. • Disturbance of hepatic lipid metabolism by oral exposure to microcystin-LR. • Crucial roles of gut microbial community shift in the metabolic disturbance induced by microcystin-LR. - Abstract: Microcystin-LR (MC-LR) can induce hepatic tissue damages and molecular toxicities, but its effects on lipid metabolism remain unknown. This study investigated the effects of MC-LR exposure on mice lipid metabolism and uncovered the underlying mechanism through metabonomic, transcriptomic and metagenomic analyses after administration of mice with MC-LR by gavage for 28 d. Increased liver weight and abdominal fat weight, and evident hepatic lipid vacuoles accumulation were observed in the mice fed with 0.2 mg/kg/d MC-LR. Serum nuclear magnetic resonance analysis showed that MC-LR treatment altered the levels of serum metabolites including triglyceride, unsaturated fatty acid (UFA) and very low density lipoprotein. Digital Gene Expression technology was used to reveal differential expression of hepatic transcriptomes, demonstrating that MC-LR treatment disturbed hepatic UFA biosynthesis and activated peroxisome proliferator-activated receptor (PPAR) signaling pathways via Pparγ, Fabp1 and Fabp2 over-expression. Metagenomic analyses of gut microbiota revealed that MC-LR exposure also increased abundant ratio of Firmicutes vs. Bacteroidetes in gut and altered biosynthetic pathways of various microbial metabolic and pro-inflammatory molecules. In conclusion, oral MC-LR exposure can induce hepatic lipid metabolism disorder mediated by UFA biosynthesis and PPAR activation, and gut microbial community shift may play an important role in the metabolic disturbance.

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.

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.

Dissecting Candida albicans Infection from the Perspective of C. albicans Virulence and Omics Approaches on Host–Pathogen Interaction: A Review

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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.

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.

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...

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.

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

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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.

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.

Integrated omics analysis of specialized metabolism in medicinal plants.

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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.

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

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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.

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 ...

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

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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.

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.

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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.

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...

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

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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. .

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

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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

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

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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.

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

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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

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

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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

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.

Fluxomics - connecting 'omics analysis and phenotypes.

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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.

Why Are Omics Technologies Important to Understanding the Role of Nutrition in Inflammatory Bowel Diseases?

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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.

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.

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

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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.

Serial-omics characterization of equine urine.

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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.

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.

Integrating Multi-omic features exploiting Chromosome Conformation Capture data

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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.

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.

[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.

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

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

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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.

Technology insight: metabonomics in gastroenterology-basic principles and potential clinical applications

DEFF Research Database (Denmark)

Bjerrum, Jacob Tveiten; Nielsen, Ole H; Wang, Yulan L

2008-01-01

Metabonomics-the study of metabolic changes in an integrated biologic system-is an emerging field. This discipline joins the other 'omics' (genomics, transcriptomics and proteomics) to give rise to a comprehensive, systems-biology approach to the evaluation of holistic in vivo function. Metabonom......Metabonomics-the study of metabolic changes in an integrated biologic system-is an emerging field. This discipline joins the other 'omics' (genomics, transcriptomics and proteomics) to give rise to a comprehensive, systems-biology approach to the evaluation of holistic in vivo function...

'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

Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

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Peter B McGarvey

2009-09-01

Full Text Available The NIAID (National Institute for Allergy and Infectious Diseases Biodefense Proteomics program aims to identify targets for potential vaccines, therapeutics, and diagnostics for agents of concern in bioterrorism, including bacterial, parasitic, and viral pathogens. The program includes seven Proteomics Research Centers, generating diverse types of pathogen-host data, including mass spectrometry, microarray transcriptional profiles, protein interactions, protein structures and biological reagents. The Biodefense Resource Center (www.proteomicsresource.org has developed a bioinformatics framework, employing a protein-centric approach to integrate and support mining and analysis of the large and heterogeneous data. Underlying this approach is a data warehouse with comprehensive protein + gene identifier and name mappings and annotations extracted from over 100 molecular databases. Value-added annotations are provided for key proteins from experimental findings using controlled vocabulary. The availability of pathogen and host omics data in an integrated framework allows global analysis of the data and comparisons across different experiments and organisms, as illustrated in several case studies presented here. (1 The identification of a hypothetical protein with differential gene and protein expressions in two host systems (mouse macrophage and human HeLa cells infected by different bacterial (Bacillus anthracis and Salmonella typhimurium and viral (orthopox pathogens suggesting that this protein can be prioritized for additional analysis and functional characterization. (2 The analysis of a vaccinia-human protein interaction network supplemented with protein accumulation levels led to the identification of human Keratin, type II cytoskeletal 4 protein as a potential therapeutic target. (3 Comparison of complete genomes from pathogenic variants coupled with experimental information on complete proteomes allowed the identification and

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

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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.

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...

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

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.

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.

DTW4Omics: comparing patterns in biological time series.

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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/.

"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.

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/.

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

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

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.

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.

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

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.

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.

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.

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.

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.

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...

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.

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.

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.

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.

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.

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.

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.

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

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

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.

Getting to the guts of the matter: the status and potential of 'omics' research of parasitic protists of the human gastrointestinal system.

Science.gov (United States)

Jex, Aaron R; Koehler, Anson V; Ansell, Brendan R; Baker, Louise; Karunajeewa, Harin; Gasser, Robin B

2013-11-01

Parasitic protists are a major cause of diarrhoeal illnesses in humans globally. Collectively, enteric pathogens exceed all other forms of infectious disease, in terms of their estimated global prevalence and socioeconomic impact. They have a disproportionately high impact on children in impoverished communities, leading to acute (diarrhoea, vomiting, dehydration and death) and chronic disease (malabsorption, malnutrition, physical and cognitive stunting and predisposition to chronic, non-communicable disease) consequences. However, historically, investment in research and disease control measures has been disproportionately poor, leading to their current classification as neglected pathogens. A sound understanding of their biology is essential in underpinning detection, treatment and control efforts. One major tool in rapidly improving our knowledge of these parasites is the use of biological systems, including 'omic' technologies. In recent years, these tools have shown significant success when applied to enteric protists. This review summarises much of this knowledge and highlights the significant remaining knowledge gaps. A major focus of the present review was to provide a perspective on a way forward to address these gaps using advanced biotechnologies. Copyright © 2013 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

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.

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.

'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

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.

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

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....

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.

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.

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...

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.

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.

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 ...

'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

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.

GeneLab: A Systems Biology Platform for Spaceflight Omics Data

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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

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.

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.

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

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

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.

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

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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.

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)

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.

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.

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.

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

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.

‘Omics’ and Plant Responses to Botrytis cinerea

Directory of Open Access Journals (Sweden)

Synan F. AbuQamar

2016-11-01

Full Text Available Botrytis cinerea is a dangerous plant pathogenic fungus with wide host ranges. This aggressive pathogen uses multiple weapons to invade and cause serious damages on its host plants. The continuing efforts of how to solve the puzzle of the multigenic nature of B. cinerea’s pathogenesis and plant defense mechanisms against the disease caused by this mold, the integration of omic approaches, including genomics, transcriptomics, proteomics and metabolomics, along with functional analysis could be a potential solution. Omic studies will provide a foundation for development of genetic manipulation and breeding programs that will eventually lead to crop improvement and protection. In this mini-review, we will highlight the current progresses in research in plant stress responses to B. cinerea using high-throughput omic technologies. We also discuss the opportunities that omic technologies can provide to research on B. cinerea-plant interactions as an example showing the impacts of omics on agricultural research.

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

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

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.

'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.

Genome-environment interactions and prospective technology assessment: evolution from pharmacogenomics to nutrigenomics and ecogenomics.

Science.gov (United States)

Ozdemir, Vural; Motulsky, Arno G; Kolker, Eugene; Godard, Béatrice

2009-02-01

The relationships between food, nutrition science, and health outcomes have been mapped over the past century. Genomic variation among individuals and populations is a new factor that enriches and challenges our understanding of these complex relationships. Hence, the confluence of nutritional science and genomics-nutrigenomics--was the focus of the OMICS: A Journal of Integrative Biology in December 2008 (Part 1). The 2009 Special Issue (Part 2) concludes the analysis of nutrigenomics research and innovations. Together, these two issues expand the scope and depth of critical scholarship in nutrigenomics, in keeping with an integrated multidisciplinary analysis across the bioscience, omics technology, social, ethical, intellectual property and policy dimensions. Historically, the field of pharmacogenetics provided the first examples of specifically identifiable gene variants predisposing to unexpected responses to drugs since the 1950s. Brewer coined the term ecogenetics in 1971 to broaden the concept of gene-environment interactions from drugs and nutrition to include environmental agents in general. In the mid-1990s, introduction of high-throughput technologies led to the terms pharmacogenomics, nutrigenomics and ecogenomics to describe, respectively, the contribution of genomic variability to differential responses to drugs, food, and environment defined in the broadest sense. The distinctions, if any, between these newer fields (e.g., nutrigenomics) and their predecessors (e.g., nutrigenetics) remain to be delineated. For nutrigenomics, its reliance on genome-wide analyses may lead to detection of new biological mechanisms governing host response to food. Recognizing "genome-environment interactions" as the conceptual thread that connects and runs through pharmacogenomics, nutrigenomics, and ecogenomics may contribute toward anticipatory governance and prospective real-time analysis of these omics fields. Such real-time analysis of omics technologies and

Health Educational Potentials of Technologies.

OpenAIRE

Magnussen, Rikke; Aagaard-Hansen, Jens

2012-01-01

The field of health promotion technology has been in an exponential growth in recent years and smart phone applications, exer-games and self-monitoring devices has become part of fitness activities and health education. In this work-in-progress-paper theoretical perspectives for categorising and analysing health educational potentials of technologies are presented.

Potential commercial applications of centrifuge technology

International Nuclear Information System (INIS)

1985-08-01

As part of an effort to prevent the loss of and maximize the use of unique developments of the centrifuge program, this document identifies and briefly describes unclassified technologies potentially available for transfer. In addition, this document presents a preliminary plan for action needed to carry out the transfer activity. Continuing efforts will provide additional descriptions of technologies which have applications that are not as apparent or as obvious as those presented here. Declassification of some of the program information, now classified as restricted data, would permit the descriptions of additional technologies which have significant commercial potential. The following are major areas of technology where transfer opportunities exist: biomedical; separation; motors and control systems; materials; vacuum; dynamics and balancing; and diagnostics and instrumentation

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

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

Global wind power potential: Physical and technological limits

International Nuclear Information System (INIS)

Castro, Carlos de; Mediavilla, Margarita; Miguel, Luis Javier; Frechoso, Fernando

2011-01-01

This paper is focused on a new methodology for the global assessment of wind power potential. Most of the previous works on the global assessment of the technological potential of wind power have used bottom-up methodologies (e.g. ). Economic, ecological and other assessments have been developed, based on these technological capacities. However, this paper tries to show that the reported regional and global technological potential are flawed because they do not conserve the energetic balance on Earth, violating the first principle of energy conservation (). We propose a top-down approach, such as that in , to evaluate the physical-geographical potential and, for the first time, to evaluate the global technological wind power potential, while acknowledging energy conservation. The results give roughly 1 TW for the top limit of the future electrical potential of wind energy. This value is much lower than previous estimates and even lower than economic and realizable potentials published for the mid-century (e.g. ). - Highlights: → Reported wind power potentials are flawed because they violate energy conservation. → For the first time, it is evaluated the technological wind power potential with a top-down approach. → Our results show 1 TWe for the limit of wind power energy, which is much lower than previous estimates.

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

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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.

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.

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

Precision medicine, an approach for development of the future medicine technologies

Directory of Open Access Journals (Sweden)

Iraj Nabipour

2016-04-01

Full Text Available Precision medicine is an approach in medicine that takes into account individual differences in people's genes, environments, and lifestyle. This field of medicine redefines our understanding of disease onset and progression, treatment response, and health outcomes through the more precise measurement of molecular, environmental, and behavioral factors that contribute to health and disease. Undoubtedly, the advances in omics technologies including genomics, data collection and storage, computational analysis, and mobile health applications over the last decade produced significant progress for precision medicine. In fact, precision medicine is a platform for the growth of personalized medicine, wearable biosensors, mobile health, computational sciences, genomic singularity, and other omics technologies. In the pathway of precision medicine, mathematics and computational sciences will be revolutionized to overcome the challenges in Big Data. By the birth of precision medicine, novel therapeutic strategies for chronic complex diseases such as cardiovascular disease and cancers would be designed in Systems Medicine.

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.

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

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

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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

Technology's Potential, Promise for Enhancing Student Learning

Science.gov (United States)

Golden, Michael

2004-01-01

Technology is a tool that has the potential to empower educational leaders at all levels--whether they are superintendents, principals, teachers, board members or state officials--as well as to redefine what education means in the 21st century. Technology provides more accurate information and advanced communication capabilities. Technology can be…

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

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.

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

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

Integration of metabolomics and transcriptomics in nanotoxicity studies.

Science.gov (United States)

Shin, Tae Hwan; Lee, Da Yeon; Lee, Hyeon-Seong; Park, Hyung Jin; Jin, Moon Suk; Paik, Man-Jeong; Manavalan, Balachandran; Mo, Jung-Soon; Lee, Gwang

2018-01-01

Biomedical research involving nanoparticles has produced useful products with medical applications. However, the potential toxicity of nanoparticles in biofluids, cells, tissues, and organisms is a major challenge. The '-omics' analyses provide molecular profiles of multifactorial biological systems instead of focusing on a single molecule. The 'omics' approaches are necessary to evaluate nanotoxicity because classical methods for the detection of nanotoxicity have limited ability in detecting miniscule variations within a cell and do not accurately reflect the actual levels of nanotoxicity. In addition, the 'omics' approaches allow analyses of in-depth changes and compensate for the differences associated with high-throughput technologies between actual nanotoxicity and results from traditional cytotoxic evaluations. However, compared with a single omics approach, integrated omics provides precise and sensitive information by integrating complex biological conditions. Thus, these technologies contribute to extended safety evaluations of nanotoxicity and allow the accurate diagnoses of diseases far earlier than was once possible in the nanotechnology era. Here, we review a novel approach for evaluating nanotoxicity by integrating metabolomics with metabolomic profiling and transcriptomics, which is termed "metabotranscriptomics". [BMB Reports 2018; 51(1): 14-20].

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

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

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.

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

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

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

Ethanol production in China: Potential and technologies

International Nuclear Information System (INIS)

Li, Shi-Zhong; Chan-Halbrendt, Catherine

2009-01-01

Rising oil demand in China has resulted in surging oil imports and mounting environmental pollution. It is projected that by 2030 the demand for fossil fuel oil will be 250 million tons. Ethanol seems to be an attractive renewable alternative to fossil fuel. This study assesses China's ethanol supply potential by examining potential non-food crops as feedstock; emerging conversion technologies; and cost competitiveness. Results of this study show that sweet sorghum among all the non-food feedstocks has the greatest potential. It grows well on the available marginal lands and the ASSF technology when commercialized will shorten the fermentation time which will lower the costs. Other emerging technologies such as improved saccharification and fermentation; and cellulosic technologies will make China more competitive in ethanol production in the future. Based on the estimated available marginal lands for energy crop production and conversion yields of the potential feedstocks, the most likely and optimistic production levels are 19 and 50 million tons of ethanol by 2020. In order to achieve those levels, the roadmap for China is to: select the non-food feedstock most suitable to grow on the available marginal land; provide funding to support the high priority conversion technologies identified by the scientists; provide monetary incentives to new and poor farmers to grow the feedstocks to revitalize rural economy; less market regulation and gradual reduction of subsidies to producers for industry efficiency; and educate consumers on the impact of fossil fuel on the environment to reduce consumption. Since the share of ethanol in the overall fuel demand is small, the impact of ethanol on lowering pollution and enhancing fuel security will be minimal. (author)

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.

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.

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.

3D Holographic Technology and Its Educational Potential

Science.gov (United States)

Lee, Hyangsook

2013-01-01

This article discusses a number of significant developments in 3D holographic technology, its potential to revolutionize aspects of teaching and learning, and challenges of implementing the technology in educational settings.

Educational Potential of Case-Study Technology

OpenAIRE

Fedorinova, Zoya; Vorobeva, Victoria; Malyanova, Marina

2015-01-01

This article presents the results of phenomenological and typological analysis of case-study technology educational potential. The definition “educational potential of case-study technology” is given, the main characteristics of which are changed in communication and collaborative activity quality, appearance of educational initiatives, change of participants’ position in learning process, formation of “collective subject” in collaborative activity, increase of learning (subject) results. Dep...

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

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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.

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.

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.

The enhanced value of combining conventional and 'omics' analyses in early assessment of drug-induced hepatobiliary injury

International Nuclear Information System (INIS)

Ellinger-Ziegelbauer, Heidrun; Adler, Melanie; Amberg, Alexander; Brandenburg, Arnd; Callanan, John J.; Connor, Susan; Fountoulakis, Michael; Gmuender, Hans; Gruhler, Albrecht; Hewitt, Philip; Hodson, Mark; Matheis, Katja A.; McCarthy, Diane; Raschke, Marian; Riefke, Bjoern; Schmitt, Christina S.; Sieber, Max; Sposny, Alexandra; Suter, Laura; Sweatman, Brian

2011-01-01

The InnoMed PredTox consortium was formed to evaluate whether conventional preclinical safety assessment can be significantly enhanced by incorporation of molecular profiling ('omics') technologies. In short-term toxicological studies in rats, transcriptomics, proteomics and metabolomics data were collected and analyzed in relation to routine clinical chemistry and histopathology. Four of the sixteen hepato- and/or nephrotoxicants given to rats for 1, 3, or 14 days at two dose levels induced similar histopathological effects. These were characterized by bile duct necrosis and hyperplasia and/or increased bilirubin and cholestasis, in addition to hepatocyte necrosis and regeneration, hepatocyte hypertrophy, and hepatic inflammation. Combined analysis of liver transcriptomics data from these studies revealed common gene expression changes which allowed the development of a potential sequence of events on a mechanistic level in accordance with classical endpoint observations. This included genes implicated in early stress responses, regenerative processes, inflammation with inflammatory cell immigration, fibrotic processes, and cholestasis encompassing deregulation of certain membrane transporters. Furthermore, a preliminary classification analysis using transcriptomics data suggested that prediction of cholestasis may be possible based on gene expression changes seen at earlier time-points. Targeted bile acid analysis, based on LC-MS metabonomics data demonstrating increased levels of conjugated or unconjugated bile acids in response to individual compounds, did not provide earlier detection of toxicity as compared to conventional parameters, but may allow distinction of different types of hepatobiliary toxicity. Overall, liver transcriptomics data delivered mechanistic and molecular details in addition to the classical endpoint observations which were further enhanced by targeted bile acid analysis using LC/MS metabonomics.

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, ...

Involvement of flocculin in negative potential-applied ITO electrode adhesion of yeast cells

Science.gov (United States)

Koyama, Sumihiro; Tsubouchi, Taishi; Usui, Keiko; Uematsu, Katsuyuki; Tame, Akihiro; Nogi, Yuichi; Ohta, Yukari; Hatada, Yuji; Kato, Chiaki; Miwa, Tetsuya; Toyofuku, Takashi; Nagahama, Takehiko; Konishi, Masaaki; Nagano, Yuriko; Abe, Fumiyoshi

2015-01-01

The purpose of this study was to develop novel methods for attachment and cultivation of specifically positioned single yeast cells on a microelectrode surface with the application of a weak electrical potential. Saccharomyces cerevisiae diploid strains attached to an indium tin oxide/glass (ITO) electrode to which a negative potential between −0.2 and −0.4 V vs. Ag/AgCl was applied, while they did not adhere to a gallium-doped zinc oxide/glass electrode surface. The yeast cells attached to the negative potential-applied ITO electrodes showed normal cell proliferation. We found that the flocculin FLO10 gene-disrupted diploid BY4743 mutant strain (flo10Δ /flo10Δ) almost completely lost the ability to adhere to the negative potential-applied ITO electrode. Our results indicate that the mechanisms of diploid BY4743 S. cerevisiae adhesion involve interaction between the negative potential-applied ITO electrode and the Flo10 protein on the cell wall surface. A combination of micropatterning techniques of living single yeast cell on the ITO electrode and omics technologies holds potential of novel, highly parallelized, microchip-based single-cell analysis that will contribute to new screening concepts and applications. PMID:26187908

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

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...

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

National Laboratory of Synchrotron Radiation: technologic potential

International Nuclear Information System (INIS)

Silva, C.E.T.G. da; Rodrigues, A.R.D.

1987-01-01

The technological or industrial developments based on the accumulated experience by research group of condensed matter physics, in Brazil, are described. The potential of a National Laboratory of Synchrotron Radiation for personnel training, absorption and adaptation of economically important technologies for Brazil, is presented. Examples of cooperations between the Laboratory and some national interprises, and some industrial applications of the synchrotron radiation are done. (M.C.K.) [pt

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.

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.

Assessment of human embryo development using morphological criteria in an era of time-lapse, algorithms and 'OMICS': is looking good still important?

Science.gov (United States)

Gardner, David K; Balaban, Basak

2016-10-01

With the worldwide move towards single embryo transfer there has been a renewed focus on the requirement for reliable means of assessing embryo viability. In an era of 'OMICS' technologies, and algorithms created through the use of time-lapse microscopy, the actual appearance of the human embryo as it progresses through each successive developmental stage to the blastocyst appears to have been somewhat neglected in recent years. Here we review the key features of the human preimplantation embryo and consider the relationship between morphological characteristics and developmental potential. Further, the impact of the culture environment on morphological traits, how key morphological qualities reflect aspects of embryo physiology, and how computer-assisted analysis of embryo morphology may facilitate a more quantitative approach to selection are discussed. The clinical introduction of time-lapse systems has reopened our eyes and given us a new vantage point from which to view the beauty of the initial stages of human life. Rather than a future in which the morphology of the embryo is deemed irrelevant, we propose that key features, such as multinucleation, cell size and blastocyst differentiation should be included in future iterations of selection/deselection algorithms. © The Author 2016. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved.For Permissions, please email: journals.permissions@oup.com.

"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.

Manipulating environmental stresses and stress tolerance of microalgae for enhanced production of lipids and value-added products-A review.

Science.gov (United States)

Chen, Bailing; Wan, Chun; Mehmood, Muhammad Aamer; Chang, Jo-Shu; Bai, Fengwu; Zhao, Xinqing

2017-11-01

Microalgae have promising potential to produce lipids and a variety of high-value chemicals. Suitable stress conditions such as nitrogen starvation and high salinity could stimulate synthesis and accumulation of lipids and high-value products by microalgae, therefore, various stress-modification strategies were developed to manipulate and optimize cultivation processes to enhance bioproduction efficiency. On the other hand, advancements in omics-based technologies have boosted the research to globally understand microalgal gene regulation under stress conditions, which enable further improvement of production efficiency via genetic engineering. Moreover, integration of multi-omics data, synthetic biology design, and genetic engineering manipulations exhibits a tremendous potential in the betterment of microalgal biorefinery. This review discusses the process manipulation strategies and omics studies on understanding the regulation of metabolite biosynthesis under various stressful conditions, and proposes genetic engineering of microalgae to improve bioproduction via manipulating stress tolerance. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metabolomics in Sepsis and Its Impact on Public Health.

Science.gov (United States)

Evangelatos, Nikolaos; Bauer, Pia; Reumann, Matthias; Satyamoorthy, Kapaettu; Lehrach, Hans; Brand, Angela

2017-01-01

Sepsis, with its often devastating consequences for patients and their families, remains a major public health concern that poses an increasing financial burden. Early resuscitation together with the elucidation of the biological pathways and pathophysiological mechanisms with the use of "-omics" technologies have started changing the clinical and research landscape in sepsis. Metabolomics (i.e., the study of the metabolome), an "-omics" technology further down in the "-omics" cascade between the genome and the phenome, could be particularly fruitful in sepsis research with the potential to alter the clinical practice. Apart from its benefit for the individual patient, metabolomics has an impact on public health that extends beyond its applications in medicine. In this review, we present recent developments in metabolomics research in sepsis, with a focus on pneumonia, and we discuss the impact of metabolomics on public health, with a focus on free/libre open source software. © 2018 S. Karger AG, Basel.

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

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.

Educational innovation, learning technologies and Virtual culture potential'

Directory of Open Access Journals (Sweden)

David Riley

2002-12-01

Full Text Available Learning technologies are regularly associated with innovative teaching but will they contribute to profound innovations in education itself? This paper addresses the question by building upon Merlin.Donald's co-evolutionary theory of mind, cognition and culture. He claimed that the invention of technologies for storing and sharing external symbol systems, such as writing, gave rise to a 'theoretic culture' with rich symbolic representations and a resultant need for formal education. More recently, Shaffer and Kaput have claimed that the development of external and shared symbol-processing technologies is giving rise to an emerging 'virtual culture'. They argue that mathematics curricula are grounded in theoretic culture and should change to meet the novel demands of 'virtual culture' for symbol-processing and representational fluency. The generic character of their cultural claim is noted in this paper and it is suggested that equivalent pedagogic arguments are applicable across the educational spectrum. Hence, four general characteristics of virtual culture are proposed, against which applications of learning technologies can be evaluated for their innovative potential. Two illustrative uses of learning technologies are evaluated in terms of their 'virtual culture potential' and some anticipated questions about this approach are discussed towards the end of the paper.

Omics Approaches for Understanding Grapevine Berry Development: Regulatory Networks Associated with Endogenous Processes and Environmental Responses

Directory of Open Access Journals (Sweden)

Alejandra Serrano

2017-09-01

Full Text Available Grapevine fruit development is a dynamic process that can be divided into three stages: formation (I, lag (II, and ripening (III, in which physiological and biochemical changes occur, leading to cell differentiation and accumulation of different solutes. These stages can be positively or negatively affected by multiple environmental factors. During the last decade, efforts have been made to understand berry development from a global perspective. Special attention has been paid to transcriptional and metabolic networks associated with the control of grape berry development, and how external factors affect the ripening process. In this review, we focus on the integration of global approaches, including proteomics, metabolomics, and especially transcriptomics, to understand grape berry development. Several aspects will be considered, including seed development and the production of seedless fruits; veraison, at which anthocyanin accumulation begins in the berry skin of colored varieties; and hormonal regulation of berry development and signaling throughout ripening, focusing on the transcriptional regulation of hormone receptors, protein kinases, and genes related to secondary messenger sensing. Finally, berry responses to different environmental factors, including abiotic (temperature, water-related stress and UV-B radiation and biotic (fungi and viruses stresses, and how they can significantly modify both, development and composition of vine fruit, will be discussed. Until now, advances have been made due to the application of Omics tools at different molecular levels. However, the potential of these technologies should not be limited to the study of single-level questions; instead, data obtained by these platforms should be integrated to unravel the molecular aspects of grapevine development. Therefore, the current challenge is the generation of new tools that integrate large-scale data to assess new questions in this field, and to support

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.

The volatile metabolome and microbiome in pulmonary and gastro-intestinal disease

NARCIS (Netherlands)

van der Schee, M.P.C.

2015-01-01

Omics-technologies allow detailed characterization of biochemical molecular families enabling data-driven and hypothesis-generating research. In this thesis we explore potential merits and pitfalls of such an approach by studying the volatile metabolome and microbiome in disease diagnosis,

Distillery spent wash: Treatment technologies and potential applications

International Nuclear Information System (INIS)

Mohana, Sarayu; Acharya, Bhavik K.; Madamwar, Datta

2009-01-01

Distillery spent wash is the unwanted residual liquid waste generated during alcohol production and pollution caused by it is one of the most critical environmental issue. Despite standards imposed on effluent quality, untreated or partially treated effluent very often finds access to watercourses. The distillery wastewater with its characteristic unpleasant odor poses a serious threat to the water quality in several regions around the globe. The ever-increasing generation of distillery spent wash on the one hand and stringent legislative regulations of its disposal on the other has stimulated the need for developing new technologies to process this effluent efficiently and economically. A number of clean up technologies have been put into practice and novel bioremediation approaches for treatment of distillery spent wash are being worked out. Potential microbial (anaerobic and aerobic) as well as physicochemical processes as feasible remediation technologies to combat environmental pollution are being explored. An emerging field in distillery waste management is exploiting its nutritive potential for production of various high value compounds. This review presents an overview of the pollution problems caused by distillery spent wash, the technologies employed globally for its treatment and its alternative use in various biotechnological sectors

Analysis of some potential social effects of four coal technologies

Energy Technology Data Exchange (ETDEWEB)

Walker, C.A.; Gould, L.C.

1980-09-01

This is an analysis of the potential social impacts of four coal technologies: conventional combustion, fluidized-bed combustion, liquifaction, and gasification. Because of their flexibility, and the abundance and relatively low costs of coal, the potential benefits of these technologies would seem to outweigh their potential social costs, both in the intermediate and long term. Nevertheless, the social costs of a coal industry are far more obscure and hard to quantify than the benefits. In general, however, it maybe expected that those technologies that can be deployed most quickly, that provide fuels that can substitute most easily for oil and natural gas, that are the cheapest, and that are the most thermally efficient will minimize social costs most in the intermediate term, while technologies that can guide energy infrastructure changes to become the most compatable with the fuels that will be most easily derived from inexhaustible sources (electricity and hydrogen) will minimize social costs most in the long run. An industry structured to favor eastern over western coal and plant sites in moderate sized communities, which could easily adapt to inexhaustible energy technologies (nuclear or solar) in the future, would be favored in either time period.

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.

Review of Potential Wind Tunnel Balance Technologies

Science.gov (United States)

Burns, Devin E.; Williams, Quincy L.; Phillips, Ben D.; Commo, Sean A.; Ponder, Jonathon D.

2016-01-01

This manuscript reviews design, manufacture, materials, sensors, and data acquisition technologies that may benefit wind tunnel balances for the aerospace research community. Current state-of-the-art practices are used as the benchmark to consider advancements driven by researcher and facility needs. Additive manufacturing is highlighted as a promising alternative technology to conventional fabrication and has the potential to reduce both the cost and time required to manufacture force balances. Material alternatives to maraging steels are reviewed. Sensor technologies including piezoresistive, piezoelectric, surface acoustic wave, and fiber optic are compared to traditional foil based gages to highlight unique opportunities and shared challenges for implementation in wind tunnel environments. Finally, data acquisition systems that could be integrated into force balances are highlighted as a way to simplify the user experience and improve data quality. In summary, a rank ordering is provided to support strategic investment in exploring the technologies reviewed in this manuscript.

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.

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;

Electromagnetic forming - a potentially viable technique for accelerator technology

International Nuclear Information System (INIS)

Rajawat, R.K.; Desai, S.V.; Kulkarni, M.R.; Dolly Rani; Nagesh, K.V.; Sethi, R.C.

2003-01-01

Modern day accelerator development encompasses a myriad technologies required for their diverse needs. Whereas RF, high voltage, vacuum, cryogenics etc., technologies meet their functional requirements, high finish lapping processes, ceramic-metal joining, oven brazing, spark erosion or wire cutting etc., are a must to meet their fabrication requirements. Electromagnetic (EM) forming technique falls in the latter category and is developed as a special technology. It is currently catering to the development as a nuclear reactor technology, but has the potential to meet accelerator requirements too. This paper highlights the general principle of its working, simple design guidelines, advantages, and suggests some specific areas where this could benefit accelerator technologies

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.

Academic medical centers as innovation ecosystems to address population -omics challenges in precision medicine.

Science.gov (United States)

Silva, Patrick J; Schaibley, Valerie M; Ramos, Kenneth S

2018-02-15

While the promise of the Human Genome Project provided significant insights into the structure of the human genome, the complexities of disease at the individual level have made it difficult to utilize -omic information in clinical decision making. Some of the existing constraints have been minimized by technological advancements that have reduced the cost of sequencing to a rate far in excess of Moore's Law (a halving in cost per unit output every 18 months). The reduction in sequencing costs has made it economically feasible to create large data commons capturing the diversity of disease across populations. Until recently, these data have primarily been consumed in clinical research, but now increasingly being considered in clinical decision- making. Such advances are disrupting common diagnostic business models around which academic medical centers (AMCs) and molecular diagnostic companies have collaborated over the last decade. Proprietary biomarkers and patents on proprietary diagnostic content are no longer driving biomarker collaborations between industry and AMCs. Increasingly the scope of the data commons and biorepositories that AMCs can assemble through a nexus of academic and pharma collaborations is driving a virtuous cycle of precision medicine capabilities that make an AMC relevant and highly competitive. A rebalancing of proprietary strategies and open innovation strategies is warranted to enable institutional precision medicine asset portfolios. The scope of the AMC's clinical trial and research collaboration portfolios with industry are increasingly dependent on the currency of data, and less on patents. Intrapeneurial support of internal service offerings, clinical trials and clinical laboratory services for example, will be important new points of emphasis at the academic-industry interface. Streamlining these new models of industry collaboration for AMCs are a new area for technology transfer offices to offer partnerships and to add value

Extracellular Enzyme Composition and Functional Characteristics of Aspergillus niger An-76 Induced by Food Processing Byproducts and Based on Integrated Functional Omics.

Science.gov (United States)

Liu, Lin; Gong, Weili; Sun, Xiaomeng; Chen, Guanjun; Wang, Lushan

2018-02-07

Byproducts of food processing can be utilized for the production of high-value-added enzyme cocktails. In this study, we utilized integrated functional omics technology to analyze composition and functional characteristics of extracellular enzymes produced by Aspergillus niger grown on food processing byproducts. The results showed that oligosaccharides constituted by arabinose, xylose, and glucose in wheat bran were able to efficiently induce the production of extracellular enzymes of A. niger. Compared with other substrates, wheat bran was more effective at inducing the secretion of β-glucosidases from GH1 and GH3 families, as well as >50% of proteases from A1-family aspartic proteases. Compared with proteins induced by single wheat bran or soybean dregs, the protein yield induced by their mixture was doubled, and the time required to reach peak enzyme activity was shortened by 25%. This study provided a technical platform for the complex formulation of various substrates and functional analysis of extracellular enzymes.

GREEN TECHNOLOGY FORESIGHT OF HIGH TECHNOLOGY: HYPE OR POTENTIALS - THE CHALLENGES FROM NANOTECHNOLOGY, BIOTECHNOLOGY AND ICT

DEFF Research Database (Denmark)

Jørgensen, Michael Søgaard

2004-01-01

The paper describes the theoretical and methodological approach in an ongoing Danish technology foresight project focusing on the environmental potentials and risks of nanotechnology, biotechnology, and information and communication technology (ICT). The paper gives a short overview of some...

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.

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.

Motorcycle crashes potentially preventable by three crash avoidance technologies on passenger vehicles.

Science.gov (United States)

Teoh, Eric R

2018-07-04

The objective of this study was to identify and quantify the motorcycle crash population that would be potential beneficiaries of 3 crash avoidance technologies recently available on passenger vehicles. Two-vehicle crashes between a motorcycle and a passenger vehicle that occurred in the United States during 2011-2015 were classified by type, with consideration of the functionality of 3 classes of passenger vehicle crash avoidance technologies: frontal crash prevention, lane maintenance, and blind spot detection. Results were expressed as the percentage of crashes potentially preventable by each type of technology, based on all known types of 2-vehicle crashes and based on all crashes involving motorcycles. Frontal crash prevention had the largest potential to prevent 2-vehicle motorcycle crashes with passenger vehicles. The 3 technologies in sum had the potential to prevent 10% of fatal 2-vehicle crashes and 23% of police-reported crashes. However, because 2-vehicle crashes with a passenger vehicle represent fewer than half of all motorcycle crashes, these technologies represent a potential to avoid 4% of all fatal motorcycle crashes and 10% of all police-reported motorcycle crashes. Refining the ability of passenger vehicle crash avoidance systems to detect motorcycles represents an opportunity to improve motorcycle safety. Expanding the capabilities of these technologies represents an even greater opportunity. However, even fully realizing these opportunities can affect only a minority of motorcycle crashes and does not change the need for other motorcycle safety countermeasures such as helmets, universal helmet laws, and antilock braking systems.

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

Assessment of foreign decommissioning technology with potential application to US decommissioning needs

International Nuclear Information System (INIS)

Allen, R.P.; Konzek, G.J.; Schneider, K.J.; Smith, R.I.

1987-09-01

This study was conducted by the Pacific Northwest Laboratory (PNL) for the US Department of Energy (DOE) to identify and technically assess foreign decommissioning technology developments that may represent significant improvements over decommissioning technology currently available or under development in the United States. Technology need areas for nuclear power reactor decommissioning operations were identified and prioritized using the results of past light water reactor (LWR) decommissioning studies to quantitatively evaluate the potential for reducing cost and decommissioning worker radiation dose for each major decommissioning activity. Based on these identified needs, current foreign decommissioning technologies of potential interest to the US were identified through personal contacts and the collection and review of an extensive body of decommissioning literature. These technologies were then assessed qualitatively to evaluate their uniqueness, potential for a significant reduction in decommissioning costs and/or worker radiation dose, development status, and other factors affecting their value and applicability to US needs

Potential alternative energy technologies on the Outer Continental Shelf.

Energy Technology Data Exchange (ETDEWEB)

Elcock, D.; Environmental Assessment

2007-04-20

This technical memorandum (TM) describes the technology requirements for three alternative energy technologies for which pilot and/or commercial projects on the U.S. Outer Continental Shelf (OCS) are likely to be proposed within the next five to seven years. For each of the alternative technologies--wind, wave, and ocean current--the TM first presents an overview. After each technology-specific overview, it describes the technology requirements for four development phases: site monitoring and testing, construction, operation, and decommissioning. For each phase, the report covers the following topics (where data are available): facility description, electricity generated, ocean area (surface and bottom) occupied, resource requirements, emissions and noise sources, hazardous materials stored or used, transportation requirements, and accident potential. Where appropriate, the TM distinguishes between pilot-scale (or demonstration-scale) facilities and commercial-scale facilities.

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.

Energy Savings Potential of Radiative Cooling Technologies

Energy Technology Data Exchange (ETDEWEB)

Fernandez, Nicholas [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Wang, Weimin [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Alvine, Kyle J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Katipamula, Srinivas [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2015-11-30

Pacific Northwest National Laboratory (PNNL), with funding from the U.S. Department of Energy’s (DOE’s) Building Technologies Program (BTP), conducted a study to estimate, through simulation, the potential cooling energy savings that could be achieved through novel approaches to capturing free radiative cooling in buildings, particularly photonic ‘selective emittance’ materials. This report documents the results of that study.

Computer technology: its potential for industrial energy conservation. A technology applications manual

Energy Technology Data Exchange (ETDEWEB)

None

1979-01-01

Today, computer technology is within the reach of practically any industrial corporation regardless of product size. This manual highlights a few of the many applications of computers in the process industry and provides the technical reader with a basic understanding of computer technology, terminology, and the interactions among the various elements of a process computer system. The manual has been organized to separate process applications and economics from computer technology. Chapter 1 introduces the present status of process computer technology and describes the four major applications - monitoring, analysis, control, and optimization. The basic components of a process computer system also are defined. Energy-saving applications in the four major categories defined in Chapter 1 are discussed in Chapter 2. The economics of process computer systems is the topic of Chapter 3, where the historical trend of process computer system costs is presented. Evaluating a process for the possible implementation of a computer system requires a basic understanding of computer technology as well as familiarity with the potential applications; Chapter 4 provides enough technical information for an evaluation. Computer and associated peripheral costs and the logical sequence of steps in the development of a microprocessor-based process control system are covered in Chapter 5.

Potential for horizontal well technology in the U.S

International Nuclear Information System (INIS)

Biglarbigi, K.; Mohan, H.; Ray, R.M.; Meehan, D.N.

2000-01-01

In the past decade, the use of horizontal well technology has increased significantly in the U.S., contributing to the drilling of 600 to 1000 horizontal oil wells annually. A total of 86 per cent of the existing horizontal wells have been drilled in three formations, the Austin chalk in Texas, the Bakken shale in North Dakota, and the Niobrara in Colorado and Wyoming. A unique analytical system has been developed by the United States Department of Energy, National Petroleum Technology Office (USDOE/NPTO) to assess the potential for greater use of horizontal well technology for other oil resources in other geological formations. The analytical system is designed to be used in association with other enhanced recovery methods that make up the DOE's Total Oil Recovery Information System (TORIS). The DOE/NPTO collaborated with industry to identify the target resource for horizontal well technology and to evaluate its future recovery potential under different economic and technological conditions. This paper provides a national summary of the potential for additional production and reserves with more diverse application of horizontal wells in various types of U.S. oil resources, including the rest of the fractured reservoirs in the Austin chalk, other fractured reservoirs in the north and northwestern states, thin-bed reservoirs, and mature waterflood field. The results were presented in terms of production, reserves and national economic benefits with a full cash-flow analysis at oil prices in the range of $16 to $24 U.S. per bbl. It is estimated that 541 million to 1 billion bbls of new reserves are economically producible at these prices. The reserves estimates pertain to future horizontal wells in known fields only and are in addition to the reserves for the existing wells as of 1 January 1998. Potential production is substantial, ranging from 50 million to 85 million bbl per year by 2004 and then declining at a rate of 8 per cent per year in the following years

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.

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.

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.

The potential use of mobile technology: enhancing accessibility and ...

African Journals Online (AJOL)

The potential use of mobile technology: enhancing accessibility and communication in a blended ... South African Journal of Education ... Recommendations, limitations of the present study, and suggestions for future research were made.

Advanced research technology for discovery of new effective compounds from Chinese herbal medicine and their molecular targets.

Science.gov (United States)

Wong, Vincent Kam-Wai; Law, Betty Yuen-Kwan; Yao, Xiao-Jun; Chen, Xi; Xu, Su Wei; Liu, Liang; Leung, Elaine Lai-Han

2016-09-01

Traditional biotechnology has been utilized by human civilization for long in wide aspects of our daily life, such as wine and vinegar production, which can generate new phytochemicals from natural products using micro-organism. Today, with advanced biotechnology, diverse applications and advantages have been exhibited not only in bringing benefits to increase the diversity and composition of herbal phytochemicals, but also helping to elucidate the treatment mechanism and accelerate new drug discovery from Chinese herbal medicine (CHM). Applications on phytochemical biotechnologies and microbial biotechnologies have been promoted to enhance phytochemical diversity. Cell labeling and imaging technology and -omics technology have been utilized to elucidate CHM treatment mechanism. Application of computational methods, such as chemoinformatics and bioinformatics provide new insights on direct target of CHM. Overall, these technologies provide efficient ways to overcome the bottleneck of CHM, such as helping to increase the phytochemical diversity, match their molecular targets and elucidate the treatment mechanism. Potentially, new oriented herbal phytochemicals and their corresponding drug targets can be identified. In perspective, tighter integration of multi-disciplinary biotechnology and computational technology will be the cornerstone to accelerate new arena formation, advancement and revolution in the fields of CHM and world pharmaceutical industry. Copyright © 2016 Elsevier Ltd. All rights reserved.

The potential impact of computer-aided assessment technology in ...

African Journals Online (AJOL)

The potential impact of computer-aided assessment technology in higher education. ... Further more 'Increased number of students in Higher Education and the ... benefits, limitations, impacts on student learning and strategies for developing ...

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.

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.

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

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.

Technology and ecological economics. Promethean technology, Pandorian potential

Energy Technology Data Exchange (ETDEWEB)

Small, Bruce [AgResearch Ltd., Private Bag 3123, Hamilton (New Zealand); Jollands, Nigel [New Zealand Centre for Ecological Economics, Massey University and Landcare Research Ltd, Private Bag 11052, Palmerston North (New Zealand)

2006-03-15

In considering social, economic and ecological impacts of new technologies it is essential to start from an understanding of human nature. This paper explores this issue drawing out some implications for ecological and neoclassical economics. The paper presents two key arguments. First, we argue that there is a growing tension between our evolved human nature and social structures and our emerging technological prowess. Modern technologies give us increasing power to manipulate the very axes of nature: space, time, energy, matter, and life. Technologies are now so powerful they give us abilities our ancestors would consider godlike. The question is posed: Are humans ready to wield the power of the gods? We have the knowledge, but do we have the wisdom? The myth of Prometheus and Pandora is considered as a metaphor for the interaction between technology, nature and universal aspects of human nature developed over eons of evolution. Second, we argue that even a 'technologically optimistic' scenario (employed by some economists) may not actually deliver Utopian outcomes. With technological advancement and diffusion there is a 'technological trickle down effect' whereby potent technologies, once available only to governments and powerful elites, become available to greater numbers of groups and individuals. The more accessible a technology, the more likely its social and ecological impacts will be shaped by the full range and extremes of human nature. These issues have implications for the development and regulation of Promethean technologies such as nuclear energy, genetic engineering and nanotechnology; technologies with unprecedented power and reach through nature. Development and diffusion of such technologies may also have implications for the ethics of the social structure of society. (author)

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.

Comprehensive two-dimensional gas chromatography and food sensory properties: potential and challenges.

Science.gov (United States)

Cordero, Chiara; Kiefl, Johannes; Schieberle, Peter; Reichenbach, Stephen E; Bicchi, Carlo

2015-01-01

Modern omics disciplines dealing with food flavor focus the analytical efforts on the elucidation of sensory-active compounds, including all possible stimuli of multimodal perception (aroma, taste, texture, etc.) by means of a comprehensive, integrated treatment of sample constituents, such as physicochemical properties, concentration in the matrix, and sensory properties (odor/taste quality, perception threshold). Such analyses require detailed profiling of known bioactive components as well as advanced fingerprinting techniques to catalog sample constituents comprehensively, quantitatively, and comparably across samples. Multidimensional analytical platforms support comprehensive investigations required for flavor analysis by combining information on analytes' identities, physicochemical behaviors (volatility, polarity, partition coefficient, and solubility), concentration, and odor quality. Unlike other omics, flavor metabolomics and sensomics include the final output of the biological phenomenon (i.e., sensory perceptions) as an additional analytical dimension, which is specifically and exclusively triggered by the chemicals analyzed. However, advanced omics platforms, which are multidimensional by definition, pose challenging issues not only in terms of coupling with detection systems and sample preparation, but also in terms of data elaboration and processing. The large number of variables collected during each analytical run provides a high level of information, but requires appropriate strategies to exploit fully this potential. This review focuses on advances in comprehensive two-dimensional gas chromatography and analytical platforms combining two-dimensional gas chromatography with olfactometry, chemometrics, and quantitative assays for food sensory analysis to assess the quality of a given product. We review instrumental advances and couplings, automation in sample preparation, data elaboration, and a selection of applications.

Potential for energy technologies in residential and commercial buildings

Energy Technology Data Exchange (ETDEWEB)

Glesk, M.M.

1979-11-01

The residential-commercial energy technology model was developed as a planning tool for policy analysis in the residential and commercial building sectors. The model and its procedures represent a detailed approach to estimating the future acceptance of energy-using technologies both in new construction and for retrofit into existing buildings. The model organizes into an analytical framework all relevant information and data on building energy technology, building markets, and government policy, and it allows for easy identification of the relative importance of key assumptions. The outputs include estimates of the degree of penetration of the various building energy technologies, the levels of energy use savings associated with them, and their costs - both private and government. The model was designed to estimate the annual energy savings associated with new technologies compared with continued use of conventional technology at 1975 levels. The amount of energy used under 1975 technology conditions is referred to as the reference case energy use. For analytical purposes the technologies were consolidated into ten groupings: electric and gas heat pumps; conservation categories I, II, and III; solar thermal (hot water, heating, and cooling); photovoltaics, and wind systems. These groupings clearly do not allow an assessment of the potential for individual technologies, but they do allow a reasonable comparison of their roles in the R/C sector. Assumptions were made regarding the technical and economic performances of the technologies over the period of the analysis. In addition, the study assessed the non-financial characteristics of the technologies - aesthetics, maintenance complexity, reliability, etc. - that will also influence their market acceptability.

Prospects for natural gas in Europe. Market potential, political intervention and technological options

International Nuclear Information System (INIS)

Kabelitz, K.R.

1997-01-01

The potential market demand, the emerging fundamental political intervention in the European gas and electricity markets and the technological options available will give the gas industry in Europe a different appearance at the beginning of the 21. century. One of the key questions is: will the political intervention and technological options and innovations assist and promote the realisation of market potential? At the moment, it cannot be stated definitely whether the currently available technological options will allow the significant cost reductions hoped for in the entire gas chain to become reality in good time. Under these circumstances, a major mismatch would emerge between the market potential predicted for natural gas in Europe and the actual market development. (R.P.)

The Potential of Using Virtual Reality Technology in Physical Activity Settings

Science.gov (United States)

Pasco, Denis

2013-01-01

In recent years, virtual reality technology has been successfully used for learning purposes. The purposes of the article are to examine current research on the role of virtual reality in physical activity settings and discuss potential application of using virtual reality technology to enhance learning in physical education. The article starts…

The potential of technology for enhancing individual placement and support supported employment.

Science.gov (United States)

Lord, Sarah E; McGurk, Susan R; Nicholson, Joanne; Carpenter-Song, Elizabeth A; Tauscher, Justin S; Becker, Deborah R; Swanson, Sarah J; Drake, Robert E; Bond, Gary R

2014-06-01

The potential of technology to enhance delivery and outcomes of Individual Placement and Support (IPS) supported employment. IPS supported employment has demonstrated robust success for improving rates of competitive employment among individuals with psychiatric disabilities. Still, a majority of those with serious mental illnesses are not employed (Bond, Drake, & Becker, 2012). The need to promote awareness of IPS and expand services is urgent. In this study, we describe ways that technologies may enhance delivery of IPS supported employment across the care continuum and stakeholder groups. Directions for research are highlighted. published literature, clinical observations, IPS learning collaborative. Technology has the potential to enhance direct service as well as workflow in the IPS supported employment process, which may lead to improved fidelity and client outcomes. Mobile and cloud technologies open opportunities for collaboration, self-directed care, and ongoing support to help clients obtain and maintain meaningful employment. Research is needed to evaluate efficacy of technology-based approaches for promoting client employment outcomes, to identify provider and organization barriers to using technology for IPS delivery, and to determine effective strategies for implementing technology with IPS in different settings and with diverse client audiences.

Capacitive technology for energy extraction from chemical potential differences

NARCIS (Netherlands)

Bastos Sales, B.

2013-01-01

This thesis introduces the principle of Capacitive energy extraction based on Donnan Potential (CDP) to exploit salinity gradients. It also shows the fundamental characterization and improvements of CDP. An alternative application of this technology aimed at thermal gradients was tested.

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.

The impact of assay technology as applied to safety assessment in reducing compound attrition in drug discovery.

Science.gov (United States)

Thomas, Craig E; Will, Yvonne

2012-02-01

Attrition in the drug industry due to safety findings remains high and requires a shift in the current safety testing paradigm. Many companies are now positioning safety assessment at each stage of the drug development process, including discovery, where an early perspective on potential safety issues is sought, often at chemical scaffold level, using a variety of emerging technologies. Given the lengthy development time frames of drugs in the pharmaceutical industry, the authors believe that the impact of new technologies on attrition is best measured as a function of the quality and timeliness of candidate compounds entering development. The authors provide an overview of in silico and in vitro models, as well as more complex approaches such as 'omics,' and where they are best positioned within the drug discovery process. It is important to take away that not all technologies should be applied to all projects. Technologies vary widely in their validation state, throughput and cost. A thoughtful combination of validated and emerging technologies is crucial in identifying the most promising candidates to move to proof-of-concept testing in humans. In spite of the challenges inherent in applying new technologies to drug discovery, the successes and recognition that we cannot continue to rely on safety assessment practices used for decades have led to rather dramatic strategy shifts and fostered partnerships across government agencies and industry. We are optimistic that these efforts will ultimately benefit patients by delivering effective and safe medications in a timely fashion.

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

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

Conditions of the potential for commercialization of the patent: the implementation of a technology public offering system technology at CNEN

International Nuclear Information System (INIS)

Archila, Daniela Lima Cerqueira

2015-01-01

This dissertation identifies the main factors which represent the conditions for the potential commercialization of patents aiming at the implementation of a system for technology public offering at CNEN as a strategy for creating licensing opportunities to the industrial sector. The method applied refers to an exploratory case study of a patented technology selected from a sample of CNEN's patent portfolio in the biopharmaceutical sector. The case study comprehends a field research of interviews conducted with two specialists in technology and innovation management, one researcher from CNEN and a biopharmaceutical company. The results show that among the nineteen main factors - related to technology, market, business and Science and Technology Organization (STO) - the market dynamics, the potential applications of the technology and an abstract of its main benefits compared to existing technologies are the major relevant information for each technology to be included in the public offering system. Other results indicate that the evaluation of such factors may be conducted by competent professionals to bring less uncertainty and risk to the early-stage of the innovation process, as well as enhance the potential interest of a company in the technology. On the other hand, the latter requires innovation capabilities to move the technology forward – additional R&D, scale-up, manufacturing and marketing - whilst the STO needs a entrepreneurial culture that mitigates its obstacles, creates more positive solutions for its routines and processes and gives sustainability to its Technology Transfer Office (TTO) through valuing its personnel in the long term. Finally, emphasis on technological partnerships with companies can be a motivating feature for directing the STO's patent strategy to the creation of proprietary technological platforms that reflect problems experienced by the commercial environment, as well as the development of this strategic patent

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

A System Model of Increasing the Investment Potential of Technologically Unrelated Sectors

Directory of Open Access Journals (Sweden)

Melnyk Alexander G.

2016-02-01

Full Text Available The article presents a theoretical substantiation and the progress of practical application of the method for evaluating lagged effects of increasing the investment potential of interaction between industries in meso-level innovation systems on the example of the high-tech sector of Ukraine. The interaction data are considered in terms of their formation in such technologically unrelated sectors as the industrial sector and sector of education and sciences. It has been determined that the analytical basis to form the models of increasing the investment potential in innovation systems of meso-level should be presented by a comprehensive integrated assessment of all sectors involved in the reproduction process including technologically unrelated sectors of highly structured innovative systems. There has been proposed a system model of increasing the investment potential of the high-tech sector taking into account the optimization and synergy effects for system decisions concerning technologically unrelated sectors in economic systems of innovation type of reproduction.

Buwchitin: a ruminal peptide with antimicrobial potential against Enterococcus faecalis

Science.gov (United States)

Oyama, Linda B.; Crochet, Jean-Adrien; Edwards, Joan E.; Girdwood, Susan E.; Cookson, Alan R.; Fernandez-Fuentes, Narcis; Hilpert, Kai; Golyshin, Peter N.; Golyshina, Olga V.; Privé, Florence; Hess, Matthias; Mantovani, Hilario C.; Creevey, Christopher J.; Huws, Sharon A.

2017-07-01

Antimicrobial peptides (AMPs) are gaining popularity as alternatives for treatment of bacterial infections and recent advances in omics technologies provide new platforms for AMP discovery. We sought to determine the antibacterial activity of a novel antimicrobial peptide, buwchitin, against Enterococcus faecalis. Buwchitin was identified from a rumen bacterial metagenome library, cloned, expressed and purified. The antimicrobial activity of the recombinant peptide was assessed using a broth microdilution susceptibility assay to determine the peptide's killing kinetics against selected bacterial strains. The killing mechanism of buwchitin was investigated further by monitoring its ability to cause membrane depolarization (diSC3(5) method) and morphological changes in E. faecalis cells. Transmission electron micrographs of buwchitin treated E. faecalis cells showed intact outer membranes with blebbing, but no major damaging effects and cell morphology changes. Buwchitin had negligible cytotoxicity against defibrinated sheep erythrocytes. Although no significant membrane leakage and depolarization was observed, buwchitin at minimum inhibitory concentration (MIC) was bacteriostatic against E. faecalis cells and inhibited growth in vitro by 70% when compared to untreated cells. These findings suggest that buwchitin, a rumen derived peptide, has potential for antimicrobial activity against E. faecalis.

Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis

Directory of Open Access Journals (Sweden)

Linda B. Oyama

2017-07-01

Full Text Available Antimicrobial peptides (AMPs are gaining popularity as alternatives for treatment of bacterial infections and recent advances in omics technologies provide new platforms for AMP discovery. We sought to determine the antibacterial activity of a novel antimicrobial peptide, buwchitin, against Enterococcus faecalis. Buwchitin was identified from a rumen bacterial metagenome library, cloned, expressed and purified. The antimicrobial activity of the recombinant peptide was assessed using a broth microdilution susceptibility assay to determine the peptide's killing kinetics against selected bacterial strains. The killing mechanism of buwchitin was investigated further by monitoring its ability to cause membrane depolarization (diSC3(5 method and morphological changes in E. faecalis cells. Transmission electron micrographs of buwchitin treated E. faecalis cells showed intact outer membranes with blebbing, but no major damaging effects and cell morphology changes. Buwchitin had negligible cytotoxicity against defibrinated sheep erythrocytes. Although no significant membrane leakage and depolarization was observed, buwchitin at minimum inhibitory concentration (MIC was bacteriostatic against E. faecalis cells and inhibited growth in vitro by 70% when compared to untreated cells. These findings suggest that buwchitin, a rumen derived peptide, has potential for antimicrobial activity against E. faecalis.

Disruptive innovation potential of the value propositions of 3D printing technology startups

DEFF Research Database (Denmark)

Jensen, Søren; Tanev, Stoyan; Hahn, Finn

2014-01-01

3D printing (or additive manufacturing) is a term used to describe the production of tangible products by using digitally controlled machine tools. The novelty of this manufacturing approach consists in the selective addition of materials layer-upon-layer, rather than through machining from solid...... material objects, moulding or casting. 3D printing (3DP) technologies have the potential to change the traditional manufacturing paradigm as well as to enable the emergence of new innovation practices based on mass customization, user design and distributed product innovation. As a result, 3DP...... potential of 3DP technology startups. The objective of this research is to empirically examine the existing business opportunities in the 3D printing technology sector. To meet this objective we have addressed two research questions: a) How do technology startups integrate new 3D printing technologies...

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.

Potential benefits of genetic modification (GM) technology for food ...

African Journals Online (AJOL)

We assessed the perception of farmers towards potential adoption of genetic modification (GM) technology for improving health, food security and agricultural productivity using a semi-structured interview. A total sample of 54 small-scale farmers participated in 6 focus group meetings (FGMs) and 23 in-depth interviews at ...

Metabolomics in epidemiology: from metabolite concentrations to integrative reaction networks.

Science.gov (United States)

Fearnley, Liam G; Inouye, Michael

2016-10-01

Metabolomics is becoming feasible for population-scale studies of human disease. In this review, we survey epidemiological studies that leverage metabolomics and multi-omics to gain insight into disease mechanisms. We outline key practical, technological and analytical limitations while also highlighting recent successes in integrating these data. The use of multi-omics to infer reaction rates is discussed as a potential future direction for metabolomics research, as a means of identifying biomarkers as well as inferring causality. Furthermore, we highlight established analysis approaches as well as simulation-based methods currently used in single- and multi-cell levels in systems biology. © The Author 2016. Published by Oxford University Press on behalf of the International Epidemiological Association.

Nano technologies, technologies converging and potential biomedical applications

International Nuclear Information System (INIS)

Capuano, V.

2005-01-01

The applications of nano technology to biology and medicine appear really promising for diagnostics, for various therapeutic approaches and in medical instrumentations. The growing synergism among nano technology, biotechnology, information technology and cognitive sciences, their convergence (NBIC) from the nano scale, could involve on next decades great changes in medicine, from a reactive to a predictive and preventive approach. It is expected that NBIC converging technologies could achieve tremendous improvements in human abilities and enhance societal achievement of related social and ethical implications, in the framework of a constant dialogue between science and society [it

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.

Configuration and technology implications of potential nuclear hydrogen system applications.

Energy Technology Data Exchange (ETDEWEB)

Conzelmann, G.; Petri, M.; Forsberg, C.; Yildiz, B.; ORNL

2005-11-05

Nuclear technologies have important distinctions and potential advantages for large-scale generation of hydrogen for U.S. energy services. Nuclear hydrogen requires no imported fossil fuels, results in lower greenhouse-gas emissions and other pollutants, lends itself to large-scale production, and is sustainable. The technical uncertainties in nuclear hydrogen processes and the reactor technologies needed to enable these processes, as well waste, proliferation, and economic issues must be successfully addressed before nuclear energy can be a major contributor to the nation's energy future. In order to address technical issues in the time frame needed to provide optimized hydrogen production choices, the Nuclear Hydrogen Initiative (NHI) must examine a wide range of new technologies, make the best use of research funding, and make early decisions on which technology options to pursue. For these reasons, it is important that system integration studies be performed to help guide the decisions made in the NHI. In framing the scope of system integration analyses, there is a hierarchy of questions that should be addressed: What hydrogen markets will exist and what are their characteristics? Which markets are most consistent with nuclear hydrogen? What nuclear power and production process configurations are optimal? What requirements are placed on the nuclear hydrogen system? The intent of the NHI system studies is to gain a better understanding of nuclear power's potential role in a hydrogen economy and what hydrogen production technologies show the most promise. This work couples with system studies sponsored by DOE-EE and other agencies that provide a basis for evaluating and selecting future hydrogen production technologies. This assessment includes identifying commercial hydrogen applications and their requirements, comparing the characteristics of nuclear hydrogen systems to those market requirements, evaluating nuclear hydrogen configuration options

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.

Enhancing innovation in agriculture at the policy level : The potential contribution of Technology Assessment

NARCIS (Netherlands)

Vanclay, Frank M.; Russell, A. Wendy; Kimber, Julie

Technology Assessment (TA) is an applied process that considers the societal implications of technological change in order to influence policy to improve technology governance. TA has considerable potential to enhance innovation in agriculture and to assist agricultural industries in becoming more

The Potential Role of Artificial Intelligence Technology in Education.

Science.gov (United States)

Salem, Abdel-Badeeh M.

The field of Artificial Intelligence (AI) and Education has traditionally a technology-based focus, looking at the ways in which AI can be used in building intelligent educational software. In addition AI can also provide an excellent methodology for learning and reasoning from the human experiences. This paper presents the potential role of AI in…

Emerging and potential technologies for facilitating shrimp peeling: A review

DEFF Research Database (Denmark)

Dang, Tem Thi; Gringer, Nina; Jessen, Flemming

2018-01-01

, ultrasound and microwave can potentially become the alternatives since they have strong peeling effects on lobsters, crabs, bivalve mollusks, eggshells, human skin, fruits and vegetables. Also these technologies offer benefits such as short process time, retained nutritional and sensorial characteristics...

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.

Unlocking the potential of smart grid technologies with behavioral science.

Science.gov (United States)

Sintov, Nicole D; Schultz, P Wesley

2015-01-01

Smart grid systems aim to provide a more stable and adaptable electricity infrastructure, and to maximize energy efficiency. Grid-linked technologies vary widely in form and function, but generally share common potentials: to reduce energy consumption via efficiency and/or curtailment, to shift use to off-peak times of day, and to enable distributed storage and generation options. Although end users are central players in these systems, they are sometimes not central considerations in technology or program design, and in some cases, their motivations for participating in such systems are not fully appreciated. Behavioral science can be instrumental in engaging end-users and maximizing the impact of smart grid technologies. In this paper, we present emerging technologies made possible by a smart grid infrastructure, and for each we highlight ways in which behavioral science can be applied to enhance their impact on energy savings.

Future-oriented technology analysis: Its potential to address disruptive transformations

OpenAIRE

Gagnin, Cristiano; Havas, Attila; Saritas, Ozcan

2011-01-01

This paper reflects on the potential of future-oriented analysis (FTA) to address major change and to support decision-makers and other stakeholders in anticipating and dealing with transformations. It does so by critically reflecting on the selected papers for this special issue as well as on the discussions that took place at the fourth Seville International Conference on Future-oriented Technology Analysis. Considering the potential roles of FTA in enabling a better understanding of co...

Clean Energy Technologies: A Preliminary Inventory of the Potential for Electricity Generation

Energy Technology Data Exchange (ETDEWEB)

Bailey, Owen; Worrell, Ernst

2005-08-03

The nation's power system is facing a diverse and broad set of challenges. These range from restructuring and increased competitiveness in power production to the need for additional production and distribution capacity to meet demand growth, and demands for increased quality and reliability of power and power supply. In addition, there are growing concerns about emissions from fossil fuel powered generation units and generators are seeking methods to reduce the CO{sub 2} emission intensity of power generation. Although these challenges may create uncertainty within the financial and electricity supply markets, they also offer the potential to explore new opportunities to support the accelerated deployment of cleaner and cost-effective technologies to meet such challenges. The federal government and various state governments, for example, support the development of a sustainable electricity infrastructure. As part of this policy, there are a variety of programs to support the development of ''cleaner'' technologies such as combined heat and power (CHP, or cogeneration) and renewable energy technologies. Energy from renewable energy sources, such as solar, wind, hydro, and biomass, are considered carbon-neutral energy technologies. The production of renewable energy creates no incremental increase in fossil fuel consumption and CO{sub 2} emissions. Electricity and thermal energy production from all renewable resources, except biomass, produces no incremental increase in air pollutants such as nitrogen oxides, sulfur oxides, particulate matter, and carbon monoxide. There are many more opportunities for the development of cleaner electricity and thermal energy technologies called ''recycled'' energy. A process using fossil fuels to produce an energy service may have residual energy waste streams that may be recycled into useful energy services. Recycled energy methods would capture energy from sources that would otherwise

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.

Genome-editing technologies and their potential application in horticultural crop breeding

Science.gov (United States)

Xiong, Jin-Song; Ding, Jing; Li, Yi

2015-01-01

Plant breeding, one of the oldest agricultural activities, parallels human civilization. Many crops have been domesticated to satisfy human's food and aesthetical needs, including numerous specialty horticultural crops such as fruits, vegetables, ornamental flowers, shrubs, and trees. Crop varieties originated through selection during early human civilization. Other technologies, such as various forms of hybridization, mutation, and transgenics, have also been invented and applied to crop breeding over the past centuries. The progress made in these breeding technologies, especially the modern biotechnology-based breeding technologies, has had a great impact on crop breeding as well as on our lives. Here, we first review the developmental process and applications of these technologies in horticultural crop breeding. Then, we mainly describe the principles of the latest genome-editing technologies and discuss their potential applications in the genetic improvement of horticultural crops. The advantages and challenges of genome-editing technologies in horticultural crop breeding are also discussed. PMID:26504570

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

Potential Impacts of Hydrokinetic and Wave Energy Conversion Technologies on Aquatic Environments

Energy Technology Data Exchange (ETDEWEB)

Čada, Glenn F.

2007-04-01

A new generation of hydropower technologies, the kinetic hydro and wave energy conversion devices, offers the possibility of generating electricity from the movements of water, without the need for dams and diversions. The Energy Policy Act of 2005 encouraged the development of these sources of renewable energy in the United States, and there is growing interest in deploying them globally. The technologies that would extract electricity from free-flowing streams, estuaries, and oceans have not been widely tested. Consequently, the U.S. Department of Energy convened a workshop to (1) identify the varieties of hydrokinetic energy and wave energy conversion devices and their stages of development, (2) identify where these technologies can best operate, (3) identify the potential environmental issues associated with these technologies and possible mitigation measures, and (4) develop a list of research needs and/or practical solutions to address unresolved environmental issues. The article reviews the results of that workshop, focusing on potential effects on freshwater, estuarine, and marine ecosystems, and we describe recent national and international developments.

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

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

Systems genetics of complex diseases using RNA-sequencing methods

DEFF Research Database (Denmark)

Mazzoni, Gianluca; Kogelman, Lisette; Suravajhala, Prashanth

2015-01-01

Next generation sequencing technologies have enabled the generation of huge quantities of biological data, and nowadays extensive datasets at different ‘omics levels have been generated. Systems genetics is a powerful approach that allows to integrate different ‘omics level and understand the bio...

Leveraging gigawatt potentials by smart heat-pump technologies using ionic liquids.

Science.gov (United States)

Wasserscheid, Peter; Seiler, Matthias

2011-04-18

One of the greatest challenges to science in the 21 st century is the development of efficient energy production, storage, and transformation systems with minimal ecological footprints. Due to the lack of efficient heat-transformation technologies, industries around the world currently waste energy in the gigawatt range at low temperatures (40-80 °C). These energy potentials can be unlocked or used more efficiently through a new generation of smart heat pumps operating with novel ionic liquid (IL)-based working pairs. The new technology is expected to allow revolutionary technical progress in heat-transformation devices, for example, significantly higher potential efficiencies, lower specific investments, and broader possibilities to incorporate waste energy from renewable sources. Furthermore, due to drastically reduced corrosion rates and excellent thermal stabilities of the new, IL-based working pairs, the high driving temperatures necessary for multi-effect cycles such as double- or triple-effect absorption chillers, can also be realized. The details of this novel and innovative heat-transformation technology are described. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genomic, Epigenomic, and Transcriptomic Profiling towards Identifying Omics Features and Specific Biomarkers That Distinguish Uterine Leiomyosarcoma and Leiomyoma at Molecular Levels

Directory of Open Access Journals (Sweden)

Tomoko Miyata

2015-01-01

Full Text Available Uterine leiomyosarcoma (LMS is the worst malignancy among the gynecologic cancers. Uterine leiomyoma (LM, a benign tumor of myometrial origin, is the most common among women of childbearing age. Because of their similar symptoms, it is difficult to preoperatively distinguish the two conditions only by ultrasound and pelvic MRI. While histopathological diagnosis is currently the main approach used to distinguish them postoperatively, unusual histologic variants of LM tend to be misdiagnosed as LMS. Therefore, development of molecular diagnosis as an alternative or confirmatory means will help to diagnose LMS more accurately. We adopted omics-based technologies to identify genome-wide features to distinguish LMS from LM and revealed that copy number, gene expression, and DNA methylation profiles successfully distinguished these tumors. LMS was found to possess features typically observed in malignant solid tumors, such as extensive chromosomal abnormalities, overexpression of cell cycle-related genes, hypomethylation spreading through large genomic regions, and frequent hypermethylation at the polycomb group target genes and protocadherin genes. We also identified candidate expression and DNA methylation markers, which will facilitate establishing postoperative molecular diagnostic tests based on conventional quantitative assays. Our results demonstrate the feasibility of establishing such tests and the possibility of developing preoperative and noninvasive methods.

NASA advanced space photovoltaic technology-status, potential and future mission applications

Science.gov (United States)

Flood, Dennis J.; Piszczor, Michael, Jr.; Stella, Paul M.; Bennett, Gary L.

1989-01-01

The NASA program in space photovoltaic research and development encompasses a wide range of emerging options for future space power systems, and includes both cell and array technology development. The long range goals are to develop technology capable of achieving 300 W/kg for planar arrays, and 300 W/sq m for concentrator arrays. InP and GaAs planar and concentrator cell technologies are under investigation for their potential high efficiency and good radiation resistance. The Advanced Photovoltaic Solar Array (APSA) program is a near term effort aimed at demonstrating 130 W/kg beginning of life specific power using thin (62 micrometer) silicon cells. It is intended to be technology transparent to future high efficiency cells and provides the baseline for development of the 300 W/kg array.

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.

CONVERGENT (NBIC TECHNOLOGIES: PROBLEMS OF DEVELOPMENT AND TRANSFORMATIONAL POTENTIAL

Directory of Open Access Journals (Sweden)

И В Данилин

2017-12-01

Full Text Available Modern innovation policy is formed under strong influence of disruptive technologies con-cepts, which help mobilize support for Science and Technology (S&T policy, structure international S&T cooperation and system, etc. They are also important for the global processes, promising changes in leading powers cohort. This is why disruptive technology concepts are accented by the emerging economics, especially by BRIC nations. A concept of converging (or nano-bio-info-cognitive, also known as NBIC technologies is very illustrative. Being originally a part of the USA nanotechnology policy and transhumanistic discourse, it gradually evolved globally with focus on “Grand Challenges”. But, despite successes of technology convergence since 2000s, concept itself proved to be not fully operational, being mostly a metaphor for rising interdisciplinarity and discipline convergence. Nonetheless its revolutionary potential was meaningful, but linked not to technological, but institu-tional and socio-cultural dimensions. Among them were human capital development, changing logic of S&T organization, reforming S&T policies, formation of new culture and ethics of research and development, systemic development of national innovation systems. These ideas, implicitly present in the NBIC concept, were of a special importance for the emerging economies as key factors for their enforced growth and rising quality of development processes. But these issues were surprisingly weak articulated in NBIC concept. Partly that was the influence of transhumanist discourse with its escape from solving societal challenges by technological change of human self. Not less important was that NBIC were seen by elites as a mean to bypass deep reforms and buildup of innovation institutions. I.e., concepts of disruptive technologies represent a psychological sub-stitute for a really intense development. Uniqueness of NBIC is that it makes this contradiction very visible. As shown in

Review of electrical energy storage technologies and systems and of their potential for the UK

Energy Technology Data Exchange (ETDEWEB)

NONE

2004-07-01

This report presents the findings of a review of current energy storage technologies and their potential application in the UK. Five groups of storage technologies are examined: compressed air energy storage; battery energy storage systems including lead-acid, nickel-cadmium, sodium-sulphur, sodium-nickel and lithium ion batteries; electrochemical flow cell systems, including the vanadium redox battery, the zinc bromide battery and the polysulphide battery; kinetic energy storage systems, ie flywheel storage; and fuel cell/electrolyser systems based on hydrogen. Details are given of the technology, its development status, potential applications and the key developers, manufacturers and suppliers. The opportunities available to UK industry and the potential for systems integration and wealth creation are also discussed.

Oil and gas technology transfer activities and potential in eight major producing states. Volume 1

Energy Technology Data Exchange (ETDEWEB)

1993-07-01

In 1990, the Interstate Oil and Gas Compact Commission (the Compact) performed a study that identified the structure and deficiencies of the system by which oil and gas producers receive information about the potential of new technologies and communicate their problems and technology needs back to the research community. The conclusions of that work were that major integrated companies have significantly more and better sources of technology information than independent producers. The majors also have significantly better mechanisms for communicating problems to the research and development (R&D) community. As a consequence, the Compact recommended analyzing potential mechanisms to improve technology transfer channels for independents and to accelerate independents acceptance and use of existing and emerging technologies. Building on this work, the Compact, with a grant from the US Department Energy, has reviewed specific technology transfer organizations in each of eight major oil producing states to identify specific R&D and technology transfer organizations, characterize their existing activities, and identify potential future activities that could be performed to enhance technology transfer to oil and gas producers. The profiles were developed based on information received from organizations,follow-up interviews, site visit and conversations, and participation in their sponsored technology transfer activities. The results of this effort are reported in this volume. In addition, the Compact has also developed a framework for the development of evaluation methodologies to determine the effectiveness of technology transfer programs in performing their intended functions and in achieving desired impacts impacts in the producing community. The results of that work are provided in a separate volume.

Music technology in music therapy - A study of the possibilities, potential and problems around the use of music technologies in music therapy with youths and adolescents

OpenAIRE

Misje, René

2013-01-01

Music technology in music therapy - A study of the possibilities, potential and problems around the use of music technologies in music therapy with youths and adolescents. This qualitative study explores the usefulness of music technology in music therapeutic practice with youth and adolescents. Four music therapist`s reflections on their use of music technologies and on the possibilities, potential and problems of this use are explored through semi-structured intervi...

Energy Savings Potential and RD&D Opportunities for Non-Vapor-Compression HVAC Technologies

Energy Technology Data Exchange (ETDEWEB)

none,

2014-03-01

While vapor-compression technologies have served heating, ventilation, and air-conditioning (HVAC) needs very effectively, and have been the dominant HVAC technology for close to 100 years, the conventional refrigerants used in vapor-compression equipment contribute to global climate change when released to the atmosphere. This Building Technologies Office report: --Identifies alternatives to vapor-compression technology in residential and commercial HVAC applications --Characterizes these technologies based on their technical energy savings potential, development status, non-energy benefits, and other factors affecting end-user acceptance and their ability to compete with conventional vapor-compression systems --Makes specific research, development, and deployment (RD&D) recommendations to support further development of these technologies, should DOE choose to support non-vapor-compression technology further.

Learning on the move: the potential impact of new mobile technologies on students’ learning

OpenAIRE

Ersoy, Alp Idil

2014-01-01

This study explores the potential use of mobile learning in higher education with a focus on student and academic staff requirements of a potential mobile application. The research examines the stakeholders’ new technology acceptance behaviour within a post-1992 university and examines how new mobile technologies are able to contribute to enhancement of the learning experience of students and additionally the roles of educators in facilitating enhancement of the learning experience.\\ud \\ud A ...

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

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.

Perspective

DEFF Research Database (Denmark)

Kussmann, Martin; Morine, Melissa J; Hager, Jörg

2013-01-01

We review here the status of human type 2 diabetes studies from a genetic, epidemiological, and clinical (intervention) perspective. Most studies limit analyses to one or a few omic technologies providing data of components of physiological processes. Since all chronic diseases are multifactorial...... at different time points along this longitudinal investigation are performed with a comprehensive set of omics platforms. These data sets are generated in a biological context, rather than biochemical compound class-driven manner, which we term "systems omics."...

Potential human factors research relating to modern technology in nuclear power plants

International Nuclear Information System (INIS)

Ketchel, J.; Fink, R.; Hanes, L.; Williges, R.; Williges, B.

1994-01-01

This paper discusses proposed human factors research to address advanced human-machine interface technology in nuclear power plants. It relates to a current EPRI project to identify a prioritized list of specific research issues that could be assessed to improve control room and other user interface areas. The project seeks to bridge the gap between the functional requirements of advanced design initiatives and the human factors research needed to support them. It seeks to identify potential benefits to be expected, as well as potential problems that might be introduced by advanced technology. It provides an organized approach to identifying human factors research needs, information already available, and measures of performance and effectiveness that might be used to assess the value of potential improvements. Those parts of the proposed plan that are subsequently approved by EPRI management and by the utility advisory committee will provide a basis for recommending research priorities

Potential applications of advanced information technology in emergency management

International Nuclear Information System (INIS)

Andersson, H.; Holmstrom, C.

1987-01-01

Within nuclear-, offshore- and petrochemical industries there is always a potential risk for severe incidents and accidents. It is a commonly shared belief that timely and correct decisions in these situations could either prevent an incident to develop into a severe accident or to mitigate the negative consequences of an accident. It is also a common belief that in those cases where poor decisions have been taken it has been because of insufficient access to information and expert knowledge when the decisions were taken. These are the background experiences for the joint Nordic research program on the use of advanced information technology in emergency preparedness organizations. Important initial research tasks in the program have been to identify and specify the needs for advanced information technology applications in emergency preparedness organizations. So far a couple of studies aiming for a needs assessment of advanced information technologies in nuclear power emergency preparedness organizations in Sweden and Finland have been completed. The conclusions from these studies are presented in this paper

Conventional engine technology. Volume 3: Comparisons and future potential

Science.gov (United States)

Dowdy, M. W.

1981-01-01

The status of five conventional automobile engine technologies was assessed and the future potential for increasing fuel economy and reducing exhaust emission was discussed, using the 1980 EPA California emisions standards as a comparative basis. By 1986, the fuel economy of a uniform charge Otto engine with a three-way catalyst is expected to increase 10%, while vehicles with lean burn (fast burn) engines should show a 20% fuel economy increase. Although vehicles with stratified-charge engines and rotary engines are expected to improve, their fuel economy will remain inferior to the other engine types. When adequate NO emissions control methods are implemented to meet the EPA requirements, vehicles with prechamber diesel engines are expected to yield a fuel economy advantage of about 15%. While successful introduction of direct injection diesel engine technology will provide a fuel savings of 30 to 35%, the planned regulation of exhaust particulates could seriously hinder this technology, because it is expected that only the smallest diesel engine vehicles could meet the proposed particulate requirements.

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

Integration of hydrogen energy technologies in stand-alone power systems analysis of the current potential for applications

International Nuclear Information System (INIS)

Zoulias, E.I.; Lymberopoulos, N.; Tsoutsos, T.; Glockner, R.; Mydske, H.J.; Vosseler, I.; Gavalda, O.; Taylor, P.

2006-01-01

The European study entitled: 'Market Potential Analysis for Introduction of Hydrogen Energy Technology in Stand-Alone Power Systems (H-SAPS)' aimed to establish a broad understanding of the market potential for H-SAPS and provide a basis for promoting in wide scale new technological applications. The scope of the study was limited to small and medium installations, up to a few hundred kW power rating and based on RE as the primary energy source. The potential for hydrogen technology in SAPS was investigated through an assessment of the technical potential for hydrogen, the market analysis and the evaluation of external factors. The results are mostly directed towards action by governments and the research community but also industry involvement is identified. The results include targeted market research, establishment of individual cost targets, regulatory changes to facilitate alternative grid solutions, information and capacity building, focused technology research and bridging the technology gaps. (author)

Advanced Communications Technology Satellite (ACTS) and potential system applications

Science.gov (United States)

Wright, David L.; Balombin, Joseph R.; Sohn, Philip Y.

1990-01-01

A description of the advanced communications technology satellite (ACTS) system is given with special emphasis on the communication characteristics. Potential satellite communications scenarios, including future operational ACTS-like satellite systems, are discussed. The description of the ACTS system updates previously published ACTS system references. Detailed information on items such as experimental ground stations is presented. The potential services can be generically described as voice, video, and data services. The implementation of these services on future operational ACTS-like systems can lead to unique quality, flexibility, and capacity characteristics at lower service costs. The specific service applications that could be supported range from low to high data rates and include both domestic and international applications.

Potential Knowledge Management Contributions to Human Performance Technology Research and Practice.

Science.gov (United States)

Schwen, Thomas M.; Kalman, Howard K.; Hara, Noriko; Kisling, Eric L.

1998-01-01

Considers aspects of knowledge management that have the potential to enhance human-performance-technology research and practice. Topics include intellectual capital; learning organization versus organizational learning; the importance of epistemology; the relationship of knowledge, learning, and performance; knowledge creation; socio-technical…

'Omics investigations of HIV and SIV pathogenesis and innate immunity.

Science.gov (United States)

Palermo, Robert E; Fuller, Deborah H

2013-01-01

In the 30 years since the advent of the AIDS epidemic, the biomedical community has put forward a battery of molecular therapies that are based on the accumulated knowledge of a limited number of viral targets. Despite these accomplishments, the community still confronts unanswered foundational questions about HIV infection. What are the cellular or biomolecular processes behind HIV pathogenesis? Can we elucidate the characteristics that distinguish those individuals who are naturally resistant to either infection or disease progression? The discovery of simian immunodeficiency viruses (SIVs) and the ensuing development of in vivo, nonhuman primate (NHP) infection models was a tremendous advance, especially in abetting the exploration of vaccine strategies. And while there have been numerous NHP infection models and vaccine trials performed, fundamental questions remain regarding host-virus interactions and immune correlates of protection. These issues are, perhaps, most starkly illustrated with the appreciation that many species of African nonhuman primates are naturally infected with strains of SIV that do not cause any appreciable disease while replicating to viral loads that match or exceed those seen with pathogenic SIV infections in Asian species of nonhuman primates. The last decade has seen the establishment of high-throughput molecular profiling tools, such as microarrays for transcriptomics, SNP arrays for genome features, and LC-MS techniques for proteins or metabolites. These provide the capacity to interrogate a biological model at a comprehensive, systems level, in contrast to historical approaches that characterized a few genes or proteins in an experiment. These methods have already had revolutionary impacts in understanding human diseases originating within the host genome such as genetic disorders and cancer, and the methods are finding increasing application in the context of infectious disease. We will provide a review of the use of such 'omics

Zero tillage: A potential technology to improve cotton yield

Directory of Open Access Journals (Sweden)

Abbas Hafiz Ghazanfar

2016-01-01

Full Text Available Zero tillage technology revealed with no use of any soil inverting technique to grow crops. The crop plant seed is planted in the soil directly after irrigation to make the soil soft without any replenishing in soil layers. A study was conducted to evaluate cotton genotypes FH-114 and FH-142 for the consecutive three years of growing seasons from 2013-15. The seed of both genotypes was sown with two date of sowing, 1 March and 1 May of each three years of sowing under three tillage treatments (zero tillage, minimum tillage and conventional tillage in triplicate completely randomized split-split plot design. It was found from results that significant differences were recorded for tillage treatments, date of sowing, genotypes and their interactions. Multivariate analysis was performed to evaluate the yield and it attributed traits for potential of FH-114 and FH-142 cotton genotypes. The genotype FH-142 was found with higher and batter performance as compared to FH-114 under zero tillage, minimum tillage and conventional tillage techniques. The traits bolls per plant, boll weight, fibre fineness, fibre strength, plant height, cotton yield per plant and sympodial branches per plant were found as most contributing traits towards cotton yield and production. It was also found that FH-142 gives higher output in terms of economic gain under zero tillage with 54% increase as compared to conventional tillage technique. It was suggested that zero tillage technology should be adopted to improve cotton yield and quality. It was also recommended that further study to evaluate zero tillage as potential technology should be performed with different regions, climate and timing throughout the world.

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.

Beyond Bitcoin: Potential Applications of Blockchain Technology in Dermatology.

Science.gov (United States)

Tung, J K; Nambudiri, V E

2018-06-26

Since its initial popularization in 2008 as the underpinnings of the digital currency Bitcoin, blockchain has seen its implications spread beyond the financial industry. 1 The field of dermatology presents promising potential applications for this burgeoning technology. Blockchain facilitates communication on a peer-to-peer platform with users sharing data directly with each other (Figure). This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

78 FR 49287 - Environmental Assessment for Potential Lease Issuance and Marine Hydrokinetic Technology Testing...

Science.gov (United States)

2013-08-13

...; MMAA104000] Environmental Assessment for Potential Lease Issuance and Marine Hydrokinetic Technology Testing... important environmental issues associated with data collection and technology testing activities (76 FR... Availability of a Revised Environmental Assessment and a Finding of No Significant Impact. SUMMARY: BOEM has...

Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated "Knowledge-Based" Platform.

Science.gov (United States)

Dubovenko, Alexey; Nikolsky, Yuri; Rakhmatulin, Eugene; Nikolskaya, Tatiana

2017-01-01

Analysis of NGS and other sequencing data, gene variants, gene expression, proteomics, and other high-throughput (OMICs) data is challenging because of its biological complexity and high level of technical and biological noise. One way to deal with both problems is to perform analysis with a high fidelity annotated knowledgebase of protein interactions, pathways, and functional ontologies. This knowledgebase has to be structured in a computer-readable format and must include software tools for managing experimental data, analysis, and reporting. Here, we present MetaCore™ and Key Pathway Advisor (KPA), an integrated platform for functional data analysis. On the content side, MetaCore and KPA encompass a comprehensive database of molecular interactions of different types, pathways, network models, and ten functional ontologies covering human, mouse, and rat genes. The analytical toolkit includes tools for gene/protein list enrichment analysis, statistical "interactome" tool for the identification of over- and under-connected proteins in the dataset, and a biological network analysis module made up of network generation algorithms and filters. The suite also features Advanced Search, an application for combinatorial search of the database content, as well as a Java-based tool called Pathway Map Creator for drawing and editing custom pathway maps. Applications of MetaCore and KPA include molecular mode of action of disease research, identification of potential biomarkers and drug targets, pathway hypothesis generation, analysis of biological effects for novel small molecule compounds and clinical applications (analysis of large cohorts of patients, and translational and personalized medicine).

DND/CAF energy horizons from historical data to the potential exploitation of emerging technologies

Energy Technology Data Exchange (ETDEWEB)

Labbe, P., E-mail: Paul.Labbe@drdc-rddc.gc.ca [Defence Research and Development Canada (DRDC), Ottawa, ON (Canada)

2015-07-01

This paper reviews the energy portfolio of Department of National Defence (DND) and of the Canadian Armed Forces (CAF) from different perspectives based on recent data analyses of the energy used over several years. Then it shows a projection of the potential impacts on current and future DND/CAF capabilities of selected emerging technologies (nuclear and non-nuclear). When possible, it estimates the potential life-cycle cost savings from the hypothetical adoption of such technologies that minimize operational cost and waste management burden. (author)

DND/CAF energy horizons from historical data to the potential exploitation of emerging technologies

Energy Technology Data Exchange (ETDEWEB)

Labbe, P. [Defence Research and Development Canada (DRDC), Ottawa, Ontario (Canada)

2016-03-15

This paper reviews the energy portfolio of Department of National Defence (DND) and of the Canadian Armed Forces (CAF) from different perspectives based on recent data analyses of the energy used over several years. Then it shows a projection of the potential impacts on current and future DND/CAF capabilities of selected emerging technologies (nuclear and non-nuclear). When possible, it estimates the potential life-cycle cost savings from the hypothetical adoption of such technologies that minimize operational cost and waste management burden. (author)

Unlocking the potential of smart grid technologies with behavioral science

Directory of Open Access Journals (Sweden)

Nicole eSintov

2015-04-01

Full Text Available Smart grid systems aim to provide a more stable and adaptable electricity infrastructure, and to maximize energy efficiency. Grid-linked technologies vary widely in form and function, but generally share common potentials: to reduce energy consumption via efficiency and/or curtailment, to shift use to off-peak times of day, and to enable distributed storage and generation options. Although end users are key players in these systems, they tend to be overlooked. Behavioral science is therefore key to engaging end-users and maximizing the impact of smart grid technologies. In this paper, we highlight several ways in which behavioral science can be applied to better understand and engage customers in smart grid systems.

MAPPING POTENTIAL TECHNOLOGY APPROPRIATE SMALL AND MEDIUM ENTERPRISES AS EFFORTS TO IMPROVE TECHNOLOGY PREPARATION LEADERSHIP IN REGION OF PONOROGO

Directory of Open Access Journals (Sweden)

Rochmat Aldy Purnomo

2017-10-01

Full Text Available Research Objectives "Mapping the Potential of Appropriate Technology for Small and Medium Enterprises as an Effort to Improve the Capability of Technology Readiness in Ponorogo District" is to describe the profile of small and medium enterprises (SMEs, evaluate and measure the level of technological readiness ability (TK2T of SMEs in Ponorogo District. The analytical tool used is a technometer that serves to measure the level of technological readiness capability used for the production of SMEs divided into three stages, basic (level 1 to level 3, medium (level 4 to level 6 and ready (Level 7 to With Level 9. By using teknometer is expected to provide basic information about mapping the potential needs and the use of appropriate technology (TTG both tools, processes and production results in Ponorogo regency. SMEs in Ponorogo Regency are dominated in the field of food, handicraft and textile fields. The SME food business unit still requires major government intervention on production process issues. The majority of SMEs business unit in the field of food still use technology (tools simple and potluck. The production process of SMEs business still neglects the hygienic side of both the production and production. The results of the evaluation and measurement of SME TK2T in Ponorogo District indicate that all samples have passed measurements at level 1 to level 3. Less than 50% pass the middle level ie level 4 to level 6, while less than 10% have passed the top level measurement , Which is level 7 to level 9. This explains that the production of SMEs in Ponorogo Regency still need government intervention both in the use of appropriate technology, as well as supporting indicators such as management, hygiene in production, human resources.

Potential of Solar-driven CDI Technology for Water Desalination in Egypt

Directory of Open Access Journals (Sweden)

Ashraf Seleym

2017-12-01

Full Text Available Freshwater scarcity is one of the most challenging problems facing the world today. Rivers, lakes, and surface ice represent only 1.2% of the fresh water sources on earth, while ground water represent over 30% of the potential fresh water. The Egyptian quota from the Nile River is limited to 55 billion m3/yr, and expected to decrease due to increasing demand of water by other Nile basin countries. According to an Egyptian government report, the total population of Egypt increased from 22 million in 1950 to around 85 million in 2010. This increase in population growth will continue for decades and it is likely to increase to between 120-150 million by 2050. Egypt has reached a state where the quantity of water available is imposing limits on its national economic development.  As indication of water scarcity, Egypt passed the international threshold value of 1000 m3/capita/year in the nineties, and it is expected to cross the threshold of absolute water scarcity of 500 m3/capita/yr by 2025. Capacitive de-ionization (CDI is a relatively new technology that was developed as recently as the late 1960s. In CDI systems, saline water is made to pass between a pair of electrodes connected to a voltage source. Ions are stored inside the pores of electrodes in CDI via the applied electric field strength. CDI is a membrane less technology, and the problems of membrane fouling in the Reverse Osmosis technology is not present in CDI. It has the potential to be energy efficient compared with other related techniques, robust technology for water desalination. This paper explores low cost and efficient desalination technologies for brackish water for irrigation and drinking purposes using the abundant solar energy in Egypt.

Potential of Solar-driven CDI Technology for Water Desalination in Egypt

Directory of Open Access Journals (Sweden)

Moustafa El Shafei

2017-12-01

Full Text Available Freshwater scarcity is one of the most challenging problems facing the world today. Rivers, lakes, and surface ice represent only 1.2% of the fresh water sources on earth, while ground water represents over 30% of the potential fresh water. The Egyptian quota from the River Nile is limited to 55 billion m/yr, and expected to decrease due to increasing demand of water by other Nile basin countries. According to an Egyptian government report, the total population of Egypt increased from 22 million in 1950 to around 85 million in 2010. This increase in population will continue for decades and it is likely to increase to between 120-150 million by 2050. Egypt has reached a state where the quantity of water available is imposing limits on its national economic development. As indication of water scarcity, Egypt passed the international threshold value of 1000 m3/capita/year in the nineties, and it is expected to cross the threshold of absolute water scarcity of 500 m3/capita/yr by 2025. Capacitive deionization (CDI is a relatively new technology that was developed as recently as the late 1960s. In CDI systems, saline water is made to pass between a pair of electrodes connected to a voltage source. Ions are stored inside the pores of electrodes in CDI via the applied electric field strength. CDI is a membrane less technology and the problems of membrane fouling in the Reverse Osmosis technology are not present in CDI. It has the potential to be energy efficient compared with other related techniques and robust technology for water desalination. This paper explores low cost and efficient desalination technologies for brackish water for irrigation and drinking purposes using the abundant solar energy in Egypt.

Integrative omic analysis reveals distinctive cold responses in leaves and roots of strawberry, Fragaria × ananassa ‘Korona’

Directory of Open Access Journals (Sweden)

Gage eKoehler

2015-10-01

Full Text Available To assess underlying metabolic processes and regulatory mechanisms during cold exposure of strawberry, integrative omic approaches were applied to Fragaria × ananassa Duch. ‘Korona’. Both root and leaf tissues were examined for responses to the cold acclimation processes. Levels of metabolites, proteins, and transcripts in tissues from plants grown at 18°C were compared to those following 1 to 10 days of cold (2°C exposure. Overall, ‘Korona’ showed a modest increase of protective metabolites such as amino acids (aspartic acid, leucine, isoleucine, and valine, pentoses, phosphorylated and non-phosphorylated hexoses, and distinct compounds of the raffinose pathway (galactinol and raffinose. By 2DE proteomics a total of 845 spots were observed in leaves; 4.6% changed significantly in response to cold.Transcript levels in leaves were determined by microarray, where dozens of cold associated transcripts were quantitatively characterized, and levels of several potential key contributors (e.g., the dehydrin COR47 and GADb to cold tolerance were confirmed by qRT-PCR. Cold responses are placed within the existing knowledge base of low temperature stress change in plants, allowing an evaluation of the uniqueness or generality of Fragaria responses in photosynthetic tissues. Overall, the cold response characteristics of ‘Korona’ are consistent with a moderately cold tolerant plant.

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

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...

Circulating MicroRNAs as Potential Biomarkers of Exercise Response

Directory of Open Access Journals (Sweden)

Mája Polakovičová

2016-10-01

Full Text Available Systematic physical activity increases physical fitness and exercise capacity that lead to the improvement of health status and athletic performance. Considerable effort is devoted to identifying new biomarkers capable of evaluating exercise performance capacity and progress in training, early detection of overtraining, and monitoring health-related adaptation changes. Recent advances in OMICS technologies have opened new opportunities in the detection of genetic, epigenetic and transcriptomic biomarkers. Very promising are mainly small non-coding microRNAs (miRNAs. miRNAs post-transcriptionally regulate gene expression by binding to mRNA and causing its degradation or inhibiting translation. A growing body of evidence suggests that miRNAs affect many processes and play a crucial role not only in cell differentiation, proliferation and apoptosis, but also affect extracellular matrix composition and maintaining processes of homeostasis. A number of studies have shown changes in distribution profiles of circulating miRNAs (c-miRNAs associated with various diseases and disorders as well as in samples taken under physiological conditions such as pregnancy or physical exercise. This overview aims to summarize the current knowledge related to the response of blood c-miRNAs profiles to different modes of exercise and to highlight their potential application as a novel class of biomarkers of physical performance capacity and training adaptation.

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.

The real-world safety potential of connected vehicle technology.

Science.gov (United States)

Doecke, Sam; Grant, Alex; Anderson, Robert W G

2015-01-01

This article estimates the safety potential of a current commercially available connected vehicle technology in real-world crashes. Data from the Centre for Automotive Safety Research's at-scene in-depth crash investigations in South Australia were used to simulate the circumstances of real-world crashes. A total of 89 crashes were selected for inclusion in the study. The crashes were selected as representative of the most prevalent crash types for injury or fatal crashes and had potential to be mitigated by connected vehicle technology. The trajectory, speeds, braking, and impact configuration of the selected in-depth cases were replicated in a software package and converted to a file format allowing "replay" of the scenario in real time as input to 2 Cohda Wireless MK2 onboard units. The Cohda Wireless onboard units are a mature connected vehicle technology that has been used in both the German simTD field trial and the U.S. Department of Transport's Safety Pilot project and have been tuned for low false alarm rates when used in the real world. The crash replay was achieved by replacing each of the onboard unit Global Positioning System (GPS) inputs with the simulated data of each of the involved vehicles. The time at which the Cohda Wireless threat detection software issued an elevated warning was used to calculate a new impact speed using 3 different reaction scenarios and 2 levels of braking. It was found that between 37 and 86% of the simulated crashes could be avoided, with highest percentage due a fully autonomous system braking at 0.7 g. The same system also reduced the impact speed relative to the actual crash in all cases. Even when a human reaction time of 1.2 s and moderate braking of 0.4 g was assumed, the impact speed was reduced in 78% of the crashes. Crash types that proved difficult for the threat detection engine were head-on crashes where the approach angle was low and right turn-opposite crashes. These results indicate that connected vehicle

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.

Industrial Waste Heat Recovery - Potential Applications, Available Technologies and Crosscutting R&D Opportunities

Energy Technology Data Exchange (ETDEWEB)

Thekdi, Arvind [E3M Inc, North Potomac, MD (United States); Nimbalkar, Sachin U. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2015-01-01

The purpose of this report was to explore key areas and characteristics of industrial waste heat and its generation, barriers to waste heat recovery and use, and potential research and development (R&D) opportunities. The report also provides an overview of technologies and systems currently available for waste heat recovery and discusses the issues or barriers for each. Also included is information on emerging technologies under development or at various stages of demonstrations, and R&D opportunities cross-walked by various temperature ranges, technology areas, and energy-intensive process industries.

Omics in Ophthalmology: Advances in Genomics and Precision Medicine for Leber Congenital Amaurosis and Age-Related Macular Degeneration.

Science.gov (United States)

den Hollander, Anneke I

2016-03-01

The genomic revolution has had a huge impact on our understanding of the genetic defects and disease mechanisms underlying ophthalmic diseases. Two examples are discussed here. The first is Leber congenital amaurosis (LCA), a severe inherited retinal dystrophy leading to severe vision loss in children, and the second is age-related macular degeneration (AMD), the most common cause of vision loss in the elderly. Twenty years ago, the genetic causes of these diseases were unknown. Currently, more than 20 LCA genes have been identified, and genetic testing can now successfully identify the genetic defects in at least 75% of all LCA cases. Gene-specific treatments have entered the clinical trial phase for three LCA genes, and for seven LCA genes gene-specific therapies have been tested in model systems. Age-related macular degeneration is a multifactorial disease caused by a combination of genetic and environmental factors. Currently, more than 40 loci have been identified for AMD, accounting for 15%-65% of the total genetic contribution to AMD. Despite the progress that has been made so far, genetic testing is not yet recommended for AMD, but this may change if we move to clinical trials or treatments that are dependent on an individual's genotype. The identification of serum or plasma biomarkers using other "-omics" technologies may further improve predictive tests and our understanding of the disease mechanisms of AMD. Ultimately, it is anticipated that predictive tests will help to stratify patients for the most suitable therapy, which will enable the development of precision medicine, tailored to individual needs.

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

Current knowledge and potential applications of cavitation technologies for the petroleum industry.

Science.gov (United States)

Avvaru, Balasubrahmanyam; Venkateswaran, Natarajan; Uppara, Parasuveera; Iyengar, Suresh B; Katti, Sanjeev S

2018-04-01

Technologies based on cavitation, produced by either ultrasound or hydrodynamic means, are part of growing literature for individual refinery unit processes. In this review, we have explained the mechanism through which these cavitation technologies intensify individual unit processes such as enhanced oil recovery, demulsification of water in oil emulsions during desalting stage, crude oil viscosity reduction, oxidative desulphurisation/demetallization, and crude oil upgrading. Apart from these refinery processes, applications of this technology are also mentioned for other potential crude oil sources such as oil shale and oil sand extraction. The relative advantages and current situation of each application/process at commercial scale is explained. Copyright © 2017 Elsevier B.V. All rights reserved.

Technology--The Extension of Human Potential

Science.gov (United States)

Childress, Vincent W.

2018-01-01

Technology is defined differently depending on one's point of view, but in "Standards for Technological Literacy," technology is defined as "Human innovation…the generation of knowledge and processes…that solve problems and extend human capabilities" (ITEA/ITEEA 2000/2002/2007). The processes associated with the development of…

Reduction Potato s hydric soil erosion using space technology

Science.gov (United States)

Guyot, E.; Rios, V.; Zelaya, D.; Rios, E.; Lepen, F.; Padilla, P.; Soria, F.

The potato's crop has an econ omic importance in Tucuman's agricultural PBI (Gross Product Income) because its rank is fourth(4°). Production's potato area is a breakable agro system; its geographic location is in Pedemonte's agro-ecological region so is essential to handle hydric erosion. Therefore, the aim of this work is improve crop's potato irrigation management through satellite information merge with farm's practices. The space technology consented to obtain Digital Model Soil using both unique differential and dual frequency GPS signals and total station. The irrigation practices were carried out due to irrigation management (FAO) and satellite imagine software (ENVI). Preliminary results of this experience allowed to follow the crop's growing through multitemporal study; reprogramming farm's irrigation practices intended for manage reduction hydric erosion and heighten economically its productivity for the next period

Metabolomics, Nutrition, and Potential Biomarkers of Food Quality, Intake, and Health Status.

Science.gov (United States)

Sébédio, Jean-Louis

Diet, dietary patterns, and other environmental factors such as exposure to toxins are playing an important role in the prevention/development of many diseases, like obesity, type 2 diabetes, and consequently on the health status of individuals. A major challenge nowadays is to identify novel biomarkers to detect as early as possible metabolic dysfunction and to predict evolution of health status in order to refine nutritional advices to specific population groups. Omics technologies such as genomics, transcriptomics, proteomics, and metabolomics coupled with statistical and bioinformatics tools have already shown great potential in this research field even if so far only few biomarkers have been validated. For the past two decades, important analytical techniques have been developed to detect as many metabolites as possible in human biofluids such as urine, blood, and saliva. In the field of food science and nutrition, many studies have been carried out for food authenticity, quality, and safety, as well as for food processing. Furthermore, metabolomic investigations have been carried out to discover new early biomarkers of metabolic dysfunction and predictive biomarkers of developing pathologies (obesity, metabolic syndrome, type-2 diabetes, etc.). Great emphasis is also placed in the development of methodologies to identify and validate biomarkers of nutrients exposure. © 2017 Elsevier Inc. All rights reserved.

High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications.

Science.gov (United States)

Ocak, S; Sos, M L; Thomas, R K; Massion, P P

2009-08-01

During the last decade, high-throughput technologies including genomic, epigenomic, transcriptomic and proteomic have been applied to further our understanding of the molecular pathogenesis of this heterogeneous disease, and to develop strategies that aim to improve the management of patients with lung cancer. Ultimately, these approaches should lead to sensitive, specific and noninvasive methods for early diagnosis, and facilitate the prediction of response to therapy and outcome, as well as the identification of potential novel therapeutic targets. Genomic studies were the first to move this field forward by providing novel insights into the molecular biology of lung cancer and by generating candidate biomarkers of disease progression. Lung carcinogenesis is driven by genetic and epigenetic alterations that cause aberrant gene function; however, the challenge remains to pinpoint the key regulatory control mechanisms and to distinguish driver from passenger alterations that may have a small but additive effect on cancer development. Epigenetic regulation by DNA methylation and histone modifications modulate chromatin structure and, in turn, either activate or silence gene expression. Proteomic approaches critically complement these molecular studies, as the phenotype of a cancer cell is determined by proteins and cannot be predicted by genomics or transcriptomics alone. The present article focuses on the technological platforms available and some proposed clinical applications. We illustrate herein how the "-omics" have revolutionised our approach to lung cancer biology and hold promise for personalised management of lung cancer.

Brain Radiation Information Data Exchange (BRIDE)

DEFF Research Database (Denmark)

Karapiperis, Christos; Kempf, Stefan J; Quintens, Roel

2016-01-01

studies. It deploys a hybrid, distributed solution using both local storage and cloud technology. Conclusions: BRIDE can act as a knowledge broker for LDIR researchers, to facilitate molecular research on the systems biology of LDIR response in mammals. Its flexible design can capture a range...... using omics technologies. Results: We describe a light-weight approach for the storage, analysis and distribution of relevant LDIR omics datasets. The data integration platform, called BRIDE, contains information from the literature as well as experimental information from transcriptomics and proteomics...

Potential use of ground-based sensor technologies for weed detection.

Science.gov (United States)

Peteinatos, Gerassimos G; Weis, Martin; Andújar, Dionisio; Rueda Ayala, Victor; Gerhards, Roland

2014-02-01

Site-specific weed management is the part of precision agriculture (PA) that tries to effectively control weed infestations with the least economical and environmental burdens. This can be achieved with the aid of ground-based or near-range sensors in combination with decision rules and precise application technologies. Near-range sensor technologies, developed for mounting on a vehicle, have been emerging for PA applications during the last three decades. These technologies focus on identifying plants and measuring their physiological status with the aid of their spectral and morphological characteristics. Cameras, spectrometers, fluorometers and distance sensors are the most prominent sensors for PA applications. The objective of this article is to describe-ground based sensors that have the potential to be used for weed detection and measurement of weed infestation level. An overview of current sensor systems is presented, describing their concepts, results that have been achieved, already utilized commercial systems and problems that persist. A perspective for the development of these sensors is given. © 2013 Society of Chemical Industry.

Adaptive remodeling of skeletal muscle energy metabolism in high-altitude hypoxia: Lessons from AltitudeOmics.

Science.gov (United States)

Chicco, Adam J; Le, Catherine H; Gnaiger, Erich; Dreyer, Hans C; Muyskens, Jonathan B; D'Alessandro, Angelo; Nemkov, Travis; Hocker, Austin D; Prenni, Jessica E; Wolfe, Lisa M; Sindt, Nathan M; Lovering, Andrew T; Subudhi, Andrew W; Roach, Robert C

2018-05-04

Metabolic responses to hypoxia play important roles in cell survival strategies and disease pathogenesis in humans. However, the homeostatic adjustments that balance changes in energy supply and demand to maintain organismal function under chronic low oxygen conditions remain incompletely understood, making it difficult to distinguish adaptive from maladaptive responses in hypoxia-related pathologies. We integrated metabolomic and proteomic profiling with mitochondrial respirometry and blood gas analyses to comprehensively define the physiological responses of skeletal muscle energy metabolism to 16 days of high-altitude hypoxia (5260 m) in healthy volunteers from the AltitudeOmics project. In contrast to the view that hypoxia down-regulates aerobic metabolism, results show that mitochondria play a central role in muscle hypoxia adaptation by supporting higher resting phosphorylation potential and enhancing the efficiency of long-chain acylcarnitine oxidation. This directs increases in muscle glucose toward pentose phosphate and one-carbon metabolism pathways that support cytosolic redox balance and help mitigate the effects of increased protein and purine nucleotide catabolism in hypoxia. Muscle accumulation of free amino acids favor these adjustments by coordinating cytosolic and mitochondrial pathways to rid the cell of excess nitrogen, but might ultimately limit muscle oxidative capacity in vivo Collectively, these studies illustrate how an integration of aerobic and anaerobic metabolism is required for physiological hypoxia adaptation in skeletal muscle, and highlight protein catabolism and allosteric regulation as unexpected orchestrators of metabolic remodeling in this context. These findings have important implications for the management of hypoxia-related diseases and other conditions associated with chronic catabolic stress. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

A comparison of graph- and kernel-based -omics data integration algorithms for classifying complex traits.

Science.gov (United States)

Yan, Kang K; Zhao, Hongyu; Pang, Herbert

2017-12-06

High-throughput sequencing data are widely collected and analyzed in the study of complex diseases in quest of improving human health. Well-studied algorithms mostly deal with single data source, and cannot fully utilize the potential of these multi-omics data sources. In order to provide a holistic understanding of human health and diseases, it is necessary to integrate multiple data sources. Several algorithms have been proposed so far, however, a comprehensive comparison of data integration algorithms for classification of binary traits is currently lacking. In this paper, we focus on two common classes of integration algorithms, graph-based that depict relationships with subjects denoted by nodes and relationships denoted by edges, and kernel-based that can generate a classifier in feature space. Our paper provides a comprehensive comparison of their performance in terms of various measurements of classification accuracy and computation time. Seven different integration algorithms, including graph-based semi-supervised learning, graph sharpening integration, composite association network, Bayesian network, semi-definite programming-support vector machine (SDP-SVM), relevance vector machine (RVM) and Ada-boost relevance vector machine are compared and evaluated with hypertension and two cancer data sets in our study. In general, kernel-based algorithms create more complex models and require longer computation time, but they tend to perform better than graph-based algorithms. The performance of graph-based algorithms has the advantage of being faster computationally. The empirical results demonstrate that composite association network, relevance vector machine, and Ada-boost RVM are the better performers. We provide recommendations on how to choose an appropriate algorithm for integrating data from multiple sources.

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...

Low-cost fabrication technologies for nanostructures: state-of-the-art and potential

International Nuclear Information System (INIS)

Santos, A; Deen, M J; Marsal, L F

2015-01-01

In the last decade, some low-cost nanofabrication technologies used in several disciplines of nanotechnology have demonstrated promising results in terms of versatility and scalability for producing innovative nanostructures. While conventional nanofabrication technologies such as photolithography are and will be an important part of nanofabrication, some low-cost nanofabrication technologies have demonstrated outstanding capabilities for large-scale production, providing high throughputs with acceptable resolution and broad versatility. Some of these nanotechnological approaches are reviewed in this article, providing information about the fundamentals, limitations and potential future developments towards nanofabrication processes capable of producing a broad range of nanostructures. Furthermore, in many cases, these low-cost nanofabrication approaches can be combined with traditional nanofabrication technologies. This combination is considered a promising way of generating innovative nanostructures suitable for a broad range of applications such as in opto-electronics, nano-electronics, photonics, sensing, biotechnology or medicine. (topical review)

Low-cost fabrication technologies for nanostructures: state-of-the-art and potential

Science.gov (United States)

Santos, A.; Deen, M. J.; Marsal, L. F.

2015-01-01

In the last decade, some low-cost nanofabrication technologies used in several disciplines of nanotechnology have demonstrated promising results in terms of versatility and scalability for producing innovative nanostructures. While conventional nanofabrication technologies such as photolithography are and will be an important part of nanofabrication, some low-cost nanofabrication technologies have demonstrated outstanding capabilities for large-scale production, providing high throughputs with acceptable resolution and broad versatility. Some of these nanotechnological approaches are reviewed in this article, providing information about the fundamentals, limitations and potential future developments towards nanofabrication processes capable of producing a broad range of nanostructures. Furthermore, in many cases, these low-cost nanofabrication approaches can be combined with traditional nanofabrication technologies. This combination is considered a promising way of generating innovative nanostructures suitable for a broad range of applications such as in opto-electronics, nano-electronics, photonics, sensing, biotechnology or medicine.

The potential use of mobile technology: enhancing accessibility and communication in a blended learning course

Directory of Open Access Journals (Sweden)

Tabisa Mayisela

2013-01-01

Full Text Available Mobile technology is increasingly being used to support blended learning beyond computer centres. It has been considered as a potential solution to the problem of a shortage of computers for accessing online learning materials (courseware in a blended learning course. The purpose of the study was to establish how the use of mobile technology could enhance accessibility and communication in a blended learning course. Data were solicitedfrom a purposive convenience sample of 36 students engaged in the blended learning course. The case study utilized a mixed-methods approach. An unstructured interview was conducted with the course lecturer and these data informed the design of the students' semi-structured questionnaire. It was found that students with access to mobile technology had an increased opportunity to access the courseware of the blended learning course. Mobile technology further enhanced student-to-student and student-to-lecturer communication by means of social networks. The study concludes that mobile technology has the potential to increase accessibility and communication in a blended learning course. Recommendations, limitations of the present study, and suggestionsforfuture research were made.

Technology transfer potential of an automated water monitoring system. [market research

Science.gov (United States)

Jamieson, W. M.; Hillman, M. E. D.; Eischen, M. A.; Stilwell, J. M.

1976-01-01

The nature and characteristics of the potential economic need (markets) for a highly integrated water quality monitoring system were investigated. The technological, institutional and marketing factors that would influence the transfer and adoption of an automated system were studied for application to public and private water supply, public and private wastewater treatment and environmental monitoring of rivers and lakes.

Towards precision prevention: Technologies for identifying healthy individuals with high risk of disease.

Science.gov (United States)

Nagel, Zachary D; Engelward, Bevin P; Brenner, David J; Begley, Thomas J; Sobol, Robert W; Bielas, Jason H; Stambrook, Peter J; Wei, Qingyi; Hu, Jennifer J; Terry, Mary Beth; Dilworth, Caroline; McAllister, Kimberly A; Reinlib, Les; Worth, Leroy; Shaughnessy, Daniel T

2017-08-01

The rise of advanced technologies for characterizing human populations at the molecular level, from sequence to function, is shifting disease prevention paradigms toward personalized strategies. Because minimization of adverse outcomes is a key driver for treatment decisions for diseased populations, developing personalized therapy strategies represent an important dimension of both precision medicine and personalized prevention. In this commentary, we highlight recently developed enabling technologies in the field of DNA damage, DNA repair, and mutagenesis. We propose that omics approaches and functional assays can be integrated into population studies that fuse basic, translational and clinical research with commercial expertise in order to accelerate personalized prevention and treatment of cancer and other diseases linked to aberrant responses to DNA damage. This collaborative approach is generally applicable to efforts to develop data-driven, individualized prevention and treatment strategies for other diseases. We also recommend strategies for maximizing the use of biological samples for epidemiological studies, and for applying emerging technologies to clinical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Handbook of systems toxicology

National Research Council Canada - National Science Library

Casciano, Daniel A; Sahu, Saura C

2011-01-01

... by internationally recognised investigators. Focusing on two rapidly developing cutting edge technologies - "omics" technology and nanotechnology with special emphasis on their applications - the scope and structure reflects...

Marine and Hydrokinetic Renewable Energy Technologies: Potential Navigational Impacts and Mitigation Measures

Energy Technology Data Exchange (ETDEWEB)

Cool, Richard, M.; Hudon, Thomas, J.; Basco, David, R.; Rondorf, Neil, E.

2009-12-10

On April 15, 2008, the Department of Energy (DOE) issued a Funding Opportunity Announcement for Advanced Water Power Projects which included a Topic Area for Marine and Hydrokinetic Renewable Energy Market Acceleration Projects. Within this Topic Area, DOE identified potential navigational impacts of marine and hydrokinetic renewable energy technologies and measures to prevent adverse impacts on navigation as a sub-topic area. DOE defines marine and hydrokinetic technologies as those capable of utilizing one or more of the following resource categories for energy generation: ocean waves; tides or ocean currents; free flowing water in rivers or streams; and energy generation from the differentials in ocean temperature. PCCI was awarded Cooperative Agreement DE-FC36-08GO18177 from the DOE to identify the potential navigational impacts and mitigation measures for marine hydrokinetic technologies, as summarized herein. The contract also required cooperation with the U.S. Coast Guard (USCG) and two recipients of awards (Pacific Energy Ventures and reVision) in a sub-topic area to develop a protocol to identify streamlined, best-siting practices. Over the period of this contract, PCCI and our sub-consultants, David Basco, Ph.D., and Neil Rondorf of Science Applications International Corporation, met with USCG headquarters personnel, with U.S. Army Corps of Engineers headquarters and regional personnel, with U.S. Navy regional personnel and other ocean users in order to develop an understanding of existing practices for the identification of navigational impacts that might occur during construction, operation, maintenance, and decommissioning. At these same meetings, “standard” and potential mitigation measures were discussed so that guidance could be prepared for project developers. Concurrently, PCCI reviewed navigation guidance published by the USCG and international community. This report summarizes the results of this effort, provides guidance in the form of a

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.

Technological and economic potential of poly(lactic acid) and lactic acid derivatives

Energy Technology Data Exchange (ETDEWEB)

Datta, R.; Tsai, S.P.; Bonsignore, P.; Moon, S.H.; Frank, J.R.

1993-10-01

Lactic acid has been an intermediate-volume specialty chemical (world production {approximately}40,000 tons/yr) used in a wide range of food processing and industrial applications. lactic acid h,as the potential of becoming a very large volume, commodity-chemical intermediate produced from renewable carbohydrates for use as feedstocks for biodegradable polymers, oxygenated chemicals, plant growth regulators, environmentally friendly ``green`` solvents, and specially chemical intermediates. In the past, efficient and economical technologies for the recovery and purification of lactic acid from crude fermentation broths and the conversion of tactic acid to the chemical or polymer intermediates had been the key technology impediments and main process cost centers. The development and deployment of novel separations technologies, such as electrodialysis (ED) with bipolar membranes, extractive distillations integrated with fermentation, and chemical conversion, can enable low-cost production with continuous processes in large-scale operations. The use of bipolar ED can virtually eliminate the salt or gypsum waste produced in the current lactic acid processes. In this paper, the recent technical advances in tactic and polylactic acid processes are discussed. The economic potential and manufacturing cost estimates of several products and process options are presented. The technical accomplishments at Argonne National Laboratory (ANL) and the future directions of this program at ANL are discussed.

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.

The future for weed control and technology.

Science.gov (United States)

Shaner, Dale L; Beckie, Hugh J

2014-09-01

This review is both a retrospective (what have we missed?) and prospective (where are we going?) examination of weed control and technology, particularly as it applies to herbicide-resistant weed management (RWM). Major obstacles to RWM are discussed, including lack of diversity in weed management, unwillingness of many weed researchers to conduct real integrated weed management research or growers to accept recommendations, influence or role of agrichemical marketing and governmental policy and lack of multidisciplinary research. We then look ahead to new technologies that are needed for future weed control in general and RWM in particular, in areas such as non-chemical and chemical weed management, novel herbicides, site-specific weed management, drones for monitoring large areas, wider application of 'omics' and simulation model development. Finally, we discuss implementation strategies for integrated weed management to achieve RWM, development of RWM for developing countries, a new classification of herbicides based on mode of metabolism to facilitate greater stewardship and greater global exchange of information to focus efforts on areas that maximize progress in weed control and RWM. There is little doubt that new or emerging technologies will provide novel tools for RMW in the future, but will they arrive in time? © 2013 Her Majesty the Queen in Right of Canada Pest Management Science © 2013 Society of Chemical Industry.

Rio Grande Erosion Potential Demonstration - Report for the National Border Technology Program; TOPICAL

International Nuclear Information System (INIS)

JEPSEN, RICHARD A.; ROBERTS, JESSE D.; LANGFORD, RICHARD; GAILANI, JOSEPH

2001-01-01

This demonstration project is a collaboration among DOE, Sandia National Laboratories, the University of Texas, El Paso (UTEP), the International Boundary and Water Commission (IBWC), and the US Army Corps of Engineers (USACE). Sandia deployed and demonstrated a field measurement technology that enables the determination of erosion and transport potential of sediments in the Rio Grande. The technology deployed was the Mobile High Shear Stress Flume. This unique device was developed by Sandia's Carlsbad Programs for the USACE and has been used extensively in collaborative efforts on near shore and river systems throughout the United States. Since surface water quantity and quality along with human health is an important part of the National Border Technology Program, technologies that aid in characterizing, managing, and protecting this valuable resource from possible contamination sources is imperative

Overview of current development in electrical energy storage technologies and the application potential in power system operation

International Nuclear Information System (INIS)

Luo, Xing; Wang, Jihong; Dooner, Mark; Clarke, Jonathan

2015-01-01

Highlights: • An overview of the state-of-the-art in Electrical Energy Storage (EES) is provided. • A comprehensive analysis of various EES technologies is carried out. • An application potential analysis of the reviewed EES technologies is presented. • The presented synthesis to EES technologies can be used to support future R and D and deployment. - Abstract: Electrical power generation is changing dramatically across the world because of the need to reduce greenhouse gas emissions and to introduce mixed energy sources. The power network faces great challenges in transmission and distribution to meet demand with unpredictable daily and seasonal variations. Electrical Energy Storage (EES) is recognized as underpinning technologies to have great potential in meeting these challenges, whereby energy is stored in a certain state, according to the technology used, and is converted to electrical energy when needed. However, the wide variety of options and complex characteristic matrices make it difficult to appraise a specific EES technology for a particular application. This paper intends to mitigate this problem by providing a comprehensive and clear picture of the state-of-the-art technologies available, and where they would be suited for integration into a power generation and distribution system. The paper starts with an overview of the operation principles, technical and economic performance features and the current research and development of important EES technologies, sorted into six main categories based on the types of energy stored. Following this, a comprehensive comparison and an application potential analysis of the reviewed technologies are presented

Exploring the potential of video technologies for collaboration in emergency medical care

DEFF Research Database (Denmark)

Sonnenwald, Diane H.; Söderholm, Hanna M.; Manning, James E.

2008-01-01

videoconferencing techniques. This may be of benefit in diagnosing and treating patients in emergency situations where specialized medical expertise is not locally available. The 3D telepresence technology does not yet exist, and there is a need to understand its potential before resources are spent on its...

Overcoming negative tendencies concerning public attitude to potentially dangerous technologies

International Nuclear Information System (INIS)

Barinov, A.; Shmelev, S.

1995-01-01

The Moscow Scientific industrial Association RADON is an enterprise with potentially dangerous technology. RADON fulfils the collection, transportation, treatment and disposal of radioactive waste from Moscow region. The inhabitants of this region consider it, and that is true, to be essentially dangerous. We understood, that it is necessary to change the situation and give the public the true information about RADON's activity. For this purpose 4 years ago we developed a new Department, the Department or External Relations

The Potential for Emerging Microbiome-Mediated Therapeutics in Asthma.

Science.gov (United States)

Ozturk, Ayse Bilge; Turturice, Benjamin Arthur; Perkins, David L; Finn, Patricia W

2017-08-10

In terms of immune regulating functions, analysis of the microbiome has led the development of therapeutic strategies that may be applicable to asthma management. This review summarizes the current literature on the gut and lung microbiota in asthma pathogenesis with a focus on the roles of innate molecules and new microbiome-mediated therapeutics. Recent clinical and basic studies to date have identified several possible therapeutics that can target innate immunity and the microbiota in asthma. Some of these drugs have shown beneficial effects in the treatment of certain asthma phenotypes and for protection against asthma during early life. Current clinical evidence does not support the use of these therapies for effective treatment of asthma. The integration of the data regarding microbiota with technologic advances, such as next generation sequencing and omics offers promise. Combining comprehensive bioinformatics, new molecules and approaches may shape future asthma treatment.

Potential Market for Satellite Technology in Meeting Telecommunication Needs of Developing Nations

Science.gov (United States)

1996-01-01

A recent study examined the potential for satellite technology to meet the telecommunication needs of developing nations. The growth of these nations depends on their attracting and holding the industrial investments of developed nations. This will not be likely with the antiquated telecommunications infrastructure typical of developing nations. On the contrary, it will require an infrastructure that is compatible with international standards. Most of the developing nations perceive this necessity and are pursuing the necessary upgrades. The rate of replacement, types of technology, services affected, and the terrestrial/satellite mix differ by each nation's priorities and gross national product (GNP).

Optical fibre temperature sensor technology and potential application in absorbed dose calorimetry

International Nuclear Information System (INIS)

Allen, P.D.; Hargrave, N.J.

1992-09-01

Optical fibre based sensors are proposed as a potential alternative to the thermistors traditionally used as temperature sensors in absorbed dose calorimetry. The development of optical fibre temperature sensor technology over the last ten years is reviewed. The potential resolution of various optical techniques is assessed with particular reference to the requirements of absorbed dose calorimetry. Attention is drawn to other issues which would require investigation before the development of practical optical fibre sensors for this purpose could occur. 192 refs., 5 tabs., 4 figs

Potential of the technology gas to liquids -GTL in Colombia

International Nuclear Information System (INIS)

Perez Angulo, Julio Cesar; Cabarcas Simancas, Manuel E; Archila Castro, Jesus; Tobias, Yamil Yubran

2005-01-01

Natural gas has a great potential because of the large reserves that currently exist at a worldwide level and because it is a cleaner source of energy than petroleum, but having the disadvantage of requiring high costs for its transportation. For this reason many alternatives have loomed for the development of reserves. Among these is the conversion of natural gas into synthetic ultra-clean fuels, called GTL, or gas-to-liquids. Through this process, Fischer-Tropsch for the production of diesel, naphtha and specialized products, which are used not only to effectively utilize natural gas reserves, but also, to cover at the need of more environmentally friendly fuels. This article will shed light on GTL technologies, presenting on a first instance an analysis of the different stages of the Fischer-Tropsch process, then the current status of this technology, afterwards the costs of investment and the necessary conditions for a project of this kind to be carried out and finally, and analysis of the applicability or projection for this technology in Colombia. Based on recent studies, it has been observed that is technology has surpassed its demonstrations stage and it is now at a maximum point of interest where companies like Sasol (the largest worldwide company in the area of synthetic carbon-based fuels), Chevron Texaco, Syntroleum, Exxon Mobil, Conoco Phillips, BP Rentech and shell. These companies have performed successful studies for the applicability of the Fischer-Tropsch technology at a large scale, and they will begin to build a number of large plants within the next few years, principally motivated by the low costs of gas and high prices of crude oil

Estimating Hydrogen Production Potential in Biorefineries Using Microbial Electrolysis Cell Technology

Energy Technology Data Exchange (ETDEWEB)

Borole, Abhijeet P [ORNL; Mielenz, Jonathan R [ORNL

2011-01-01

Microbial electrolysis cells (MECs) are devices that use a hybrid biocatalysis-electrolysis process for production of hydrogen from organic matter. Future biofuel and bioproducts industries are expected to generate significant volumes of waste streams containing easily degradable organic matter. The emerging MEC technology has potential to derive added- value from these waste streams via production of hydrogen. Biorefinery process streams, particularly the stillage or distillation bottoms contain underutilized sugars as well as fermentation and pretreatment byproducts. In a lignocellulosic biorefinery designed for producing 70 million gallons of ethanol per year, up to 7200 m3/hr of hydrogen can be generated. The hydrogen can either be used as an energy source or a chemical reagent for upgrading and other reactions. The energy content of the hydrogen generated is sufficient to meet 57% of the distillation energy needs. We also report on the potential for hydrogen production in existing corn mills and sugar-based biorefineries. Removal of the organics from stillage has potential to facilitate water recycle. Pretreatment and fermentation byproducts generated in lignocellulosic biorefinery processes can accumulate to highly inhibitory levels in the process streams, if water is recycled. The byproducts of concern including sugar- and lignin- degradation products such as furans and phenolics can also be converted to hydrogen in MECs. We evaluate hydrogen production from various inhibitory byproducts generated during pretreatment of various types of biomass. Finally, the research needs for development of the MEC technology and aspects particularly relevant to the biorefineries are discussed.

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

The first decade of MALDI protein profiling

DEFF Research Database (Denmark)

Albrethsen, Jakob

2011-01-01

MALDI protein profiling has identified several important challenges in omics-based biomarker research. First, research into the analytical performance of a novel omics-platform of potential diagnostic impact must be carried out in a critical manner and according to common guidelines. Evaluation s...

Potential of robots as next-generation technology for clinical assessment of neurological disorders and upper-limb therapy.

Science.gov (United States)

Scott, Stephen H; Dukelow, Sean P

2011-01-01

Robotic technologies have profoundly affected the identification of fundamental properties of brain function. This success is attributable to robots being able to control the position of or forces applied to limbs, and their inherent ability to easily, objectively, and reliably quantify sensorimotor behavior. Our general hypothesis is that these same attributes make robotic technologies ideal for clinically assessing sensory, motor, and cognitive impairments in stroke and other neurological disorders. Further, they provide opportunities for novel therapeutic strategies. The present opinionated review describes how robotic technologies combined with virtual/augmented reality systems can support a broad range of behavioral tasks to objectively quantify brain function. This information could potentially be used to provide more accurate diagnostic and prognostic information than is available from current clinical assessment techniques. The review also highlights the potential benefits of robots to provide upper-limb therapy. Although the capital cost of these technologies is substantial, it pales in comparison with the potential cost reductions to the overall healthcare system that improved assessment and therapeutic interventions offer.

NASA's Vision for Potential Energy Reduction from Future Generations of Propulsion Technology

Science.gov (United States)

Haller, Bill

2015-01-01

Through a robust partnership with the aviation industry, over the past 50 years NASA programs have helped foster advances in propulsion technology that enabled substantial reductions in fuel consumption for commercial transports. Emerging global trends and continuing environmental concerns are creating challenges that will very likely transform the face of aviation over the next 20-40 years. In recognition of this development, NASA Aeronautics has established a set of Research Thrusts that will help define the future direction of the agency's research technology efforts. Two of these thrusts, Ultra-Efficient Commercial Vehicles and Transition to Low-Carbon Propulsion, serve as cornerstones for the Advanced Air Transport Technology (AATT) project. The AATT project is exploring and developing high-payoff technologies and concepts that are key to continued improvement in energy efficiency and environmental compatibility for future generations of fixed-wing, subsonic transports. The AATT project is primarily focused on the N+3 timeframe, or 3 generations from current technology levels. As should be expected, many of the propulsion system architectures technologies envisioned for N+3 vary significantly from todays engines. The use of batteries in a hybrid-electric configuration or deploying multiple fans distributed across the airframe to enable higher bypass ratios are just two examples of potential advances that could enable substantial energy reductions over current propulsion systems.

Review of potential subsurface permeable barrier emplacement and monitoring technologies

International Nuclear Information System (INIS)

Riggsbee, W.H.; Treat, R.L.; Stansfield, H.J.; Schwarz, R.M.; Cantrell, K.J.; Phillips, S.J.

1994-02-01

This report focuses on subsurface permeable barrier technologies potentially applicable to existing waste disposal sites. This report describes candidate subsurface permeable barriers, methods for emplacing these barriers, and methods used to monitor the barrier performance. Two types of subsurface barrier systems are described: those that apply to contamination.in the unsaturated zone, and those that apply to groundwater and to mobile contamination near the groundwater table. These barriers may be emplaced either horizontally or vertically depending on waste and site characteristics. Materials for creating permeable subsurface barriers are emplaced using one of three basic methods: injection, in situ mechanical mixing, or excavation-insertion. Injection is the emplacement of dissolved reagents or colloidal suspensions into the soil at elevated pressures. In situ mechanical mixing is the physical blending of the soil and the barrier material underground. Excavation-insertion is the removal of a soil volume and adding barrier materials to the space created. Major vertical barrier emplacement technologies include trenching-backfilling; slurry trenching; and vertical drilling and injection, including boring (earth augering), cable tool drilling, rotary drilling, sonic drilling, jetting methods, injection-mixing in drilled holes, and deep soil mixing. Major horizontal barrier emplacement technologies include horizontal drilling, microtunneling, compaction boring, horizontal emplacement, longwall mining, hydraulic fracturing, and jetting methods

The potential environmental gains from recycling waste plastics: Simulation of transferring recycling and recovery technologies to Shenyang, China

International Nuclear Information System (INIS)

Chen Xudong; Xi Fengming; Geng Yong; Fujita, Tsuyoshi

2011-01-01

Research highlights: → Urban symbiosis creates compatibility of industrial development and waste management. → Mechanical technology leads to more CO 2 emission reduction. → Energy recovery technology leads to more fossil fuel saving. → Clean energy makes recycling technologies cleaner. → Demand management is crucial for realizing potential environmental gains of recycling. - Abstract: With the increasing attention on developing a low-carbon economy, it is necessary to seek appropriate ways on reducing greenhouse gas (GHG) emissions through innovative municipal solid waste management (MSWM), such as urban symbiosis. However, quantitative assessments on the environmental benefits of urban symbiosis, especially in developing countries, are limited because only a limited number of planned synergistic activities have been successful and it is difficult to acquire detailed inventory data from private companies. This paper modifies and applies a two-step simulation system and used it to assess the potential environmental benefits, including the reduction of GHG emissions and saving of fossil fuels, by employing various Japanese plastics recycling/energy-recovery technologies in Shenyang, China. The results showed that among various recycling/energy-recovery technologies, the mechanical waste plastics recycling technology, which produces concrete formwork boards (NF boards), has the greatest potential in terms of reducing GHG emissions (1.66 kg CO 2 e/kg plastics), whereas the technology for the production of refuse plastic fuel (RPF) has the greatest potential on saving fossil fuel consumption (0.77 kgce/kg-plastics). Additional benefits can be gained by applying combined technologies that cascade the utilization of waste plastics. Moreover, the development of clean energy in conjunction with the promotion of new waste plastics recycling programs could contribute to additional reductions in GHG emissions and fossil fuel consumption.

The potential of natural gas as a bridging technology in low-emission road transportation in Germany

Directory of Open Access Journals (Sweden)

Wang-Helmreich Hanna

2012-01-01

Full Text Available Greenhouse gas emission reductions are at the centre of national and international efforts to mitigate climate change. In road transportation, many politically incentivised measures focus on increasing the energy efficiency of established technologies, or promoting electric or hybrid vehicles. The abatement potential of the former approach is limited, electric mobility technologies are not yet market-ready. In a case study for Germany, this paper focuses on natural gas powered vehicles as a bridging technology in road transportation. Scenario analyses with a low level of aggregation show that natural gas-based road transportation in Germany can accumulate up to 464 million tonnes of CO2-equivalent emission reductions until 2030 depending on the speed of the diffusion process. If similar policies were adopted EU-wide, the emission reduction potential could reach a maximum of about 2.5 billion tonnes of CO2-equivalent. Efforts to promote natural gas as a bridging technology may therefore contribute to significant emissions reductions.

Elusive prize: enormous coal gas potential awaits production technology breakthrough

Energy Technology Data Exchange (ETDEWEB)

Collison, M.

2002-01-07

The expanded gas pipeline grid has excess capacity, and gas resources are declining. There is increasing interest in development of Canada's resources of coalbed methane (CBM). The chairman of the Canadian Coalbed Methane Forum estimates that Canada has more than 3,000 trillion ft{sup 3} of gas awaiting suitable technology. PanCanadian and MGV Energy conducted a CBM exploration and pilot study on the Palliser spread in southern Alberta. Results from 23 of 75 wells are encouraging. The study is being accelerated and expanded to include an additional 50 wells elsewhere in Alberta. Some scientists anticipate commercial CBM production within two years. Problems facing developers include the large land holdings necessary for economic CBM production and the disposal of coal formation water. It is anticipated that U.S. technology will be modified and used. The potential for CBM development at Pictou in Nova Scotia and in British Columbia in the foothills is considered. 3 figs.

Hybrid Vehicle Technologies and their potential for reducing oil use

Science.gov (United States)

German, John

2006-04-01

Vehicles with hybrid gasoline-electric powertrains are starting to gain market share. Current hybrid vehicles add an electric motor, battery pack, and power electronics to the conventional powertrain. A variety of engine/motor configurations are possible, each with advantages and disadvantages. In general, efficiency is improved due to engine shut-off at idle, capture of energy during deceleration that is normally lost as heat in the brakes, downsizing of the conventional engine, and, in some cases, propulsion on the electric motor alone. Ongoing increases in hybrid market share are dependent on cost reduction, especially the battery pack, efficiency synergies with other vehicle technologies, use of the high electric power to provide features desired by customers, and future fuel price and availability. Potential barriers include historically low fuel prices, high discounting of the fuel savings by new vehicle purchasers, competing technologies, and tradeoffs with other factors desired by customers, such as performance, utility, safety, and luxury features.

Innate and adaptive immunity in the development of depression: An update on current knowledge and technological advances.

Science.gov (United States)

Haapakoski, Rita; Ebmeier, Klaus P; Alenius, Harri; Kivimäki, Mika

2016-04-03

The inflammation theory of depression, proposed over 20years ago, was influenced by early studies on T cell responses and since then has been a stimulus for numerous research projects aimed at understanding the relationship between immune function and depression. Observational studies have shown that indicators of immunity, especially C reactive protein and proinflammatory cytokines, such as interleukin 6, are associated with an increased risk of depressive disorders, although the evidence from randomized trials remains limited and only few studies have assessed the interplay between innate and adaptive immunity in depression. In this paper, we review current knowledge on the interactions between central and peripheral innate and adaptive immune molecules and the potential role of immune-related activation of microglia, inflammasomes and indoleamine-2,3-dioxygenase in the development of depressive symptoms. We highlight how combining basic immune methods with more advanced 'omics' technologies would help us to make progress in unravelling the complex associations between altered immune function and depressive disorders, in the identification of depression-specific biomarkers and in developing immunotherapeutic treatment strategies that take individual variability into account. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

The impact of post-genomics approaches in neurodegenerative demyelinating diseases: the case of Guillain-Barré syndrome.

Science.gov (United States)

Villar, Margarita; Mateos-Hernandez, Lourdes; de la Fuente, Jose

2018-03-14

Why an autoimmune disease that is the main cause of the acute neuromuscular paralysis worldwide has not yet a well-characterized cause or an effective treatment? The existence of different clinical variants for the Guillain-Barré syndrome (GBS) coupled with the fact that a high number of pathogens can cause an infection that sometimes, but not always, precedes the development of the syndrome, confers a high degree of uncertainty for both prognosis and treatment. In the post-genomic era, the development of omics technologies for the high-throughput analysis of biological molecules is allowing the characterization of biological systems in a degree of depth unimaginable before. In this context, this work summarize the application of post-genomics technologies to the study of GBS. We performed a structured search of bibliographic databases for peer-reviewed research literature to outline the state of the art with regard the application of post-genomics technologies to the study of GBS. The quality of retrieved papers was assessed using standard tools and thirty-four were included in the review. To date, transcriptomics and proteomics have been the unique post-genomics approaches applied to GBS study. Most of these studies have been performed on cerebrospinal fluid samples and only few studies have been conducted with other samples such as serum, Schwann cells and human peripheral nerve. In the post-genomics era, transcriptomics and proteomics have shown the possibilities that omics technologies can offer for a better understanding of the immunological and pathological mechanisms involved in GBS and the identification of potential biomarkers, but these results have only shown the tip of the iceberg and there is still a long way to exploit the full potential that post-genomics approaches could offer to the study of the GBS. The integration of different omics datasets through a systems biology approach could allow network-based analyses to describe the complexity and

Renewable energy technologies in the Maldives - Realizing the potential

International Nuclear Information System (INIS)

Alphen, Klaas van; Hekkert, Marko P.; Sark, Wilfried G.J.H.M. van

2008-01-01

Like in many Small Island Developing States, the techno-economic potential of renewable energy technologies (RETs) in the Maldives is substantial. However, it is not certain that these economically viable RETs will indeed be implemented and utilized, since this is greatly influenced by various social, institutional and political factors (i.e., the Innovation System). In order to steer away from activities that enhance the current fossil fuel based lock-in situation and create an environment that increases the chance of a successful transfer and diffusion of RETs, several projects have been set up in the Maldives. These projects have been initiated by the Global Environmental Facility, the United Nations Development Program, and the European Commission. In this article we evaluate these projects by analyzing whether or not they strengthen the local Renewable Energy Innovation System. This evaluation shows that these RE programs strengthen most of the key processes necessary in an Innovation System conducive to technology transfer. However, as not enough attention is being paid to local entrepreneurial activities and the creation of a domestic market for RETs, the process of RET transfer might run the risk of stagnation after completion of the RE programs. (author)

The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining

Directory of Open Access Journals (Sweden)

Dóra Szakonyi

2015-05-01

DATA: The presented work was performed in the framework of the AGRON-OMICS project (Arabidopsis GRO wth Network integrating OMICS technologies supported by European Commission 6th Framework Programme project (Grant number LSHG-CT-2006-037704. This is a data integration and data sharing portal collecting all the all the major results from the consortium. All data presented in our paper is available here. https://agronomics.ethz.ch/.

‘Omics’ technologies in quantitative microbial risk assessment

NARCIS (Netherlands)

Brul, S.; Basset, J.; Cook, P.; Kathariou, S.; McClure, P.; Jasti, P.R.; Betts, R.

2012-01-01

‘Omics’ tools are being developed at an ever increasing pace. Collectively, genome sequencing, genome-wide transcriptional analysis (transcriptomics), proteomics, metabolomics, flux analysis (‘fluxomics’) and other applications are captured under the term omics. The data generated using these tools

HTR process heat applications, status of technology and economical potential

International Nuclear Information System (INIS)

Barnet, H.

1997-01-01

The technical and industrial feasibility of the production of high temperature heat from nuclear fuel is presented. The technical feasibility of high temperature heat consuming processes is reviewed and assessed. The conclusion is drawn that the next technological step for pilot plant scale demonstration is the nuclear heated steam reforming process. The economical potential of HTR process heat applications is reviewed: It is directly coupled to the economical competitiveness of HTR electricity production. Recently made statements and pre-conditions on the economic competitiveness in comparison to world market coal are reported. (author). 8 figs

Engineered Nanomaterials, Sexy New Technology and Potential Hazards

International Nuclear Information System (INIS)

Beaulieu, R.A.

2009-01-01

Engineered nanomaterials enhance exciting new applications that can greatly benefit society in areas of cancer treatments, solar energy, energy storage, and water purification. While nanotechnology shows incredible promise in these and other areas by exploiting nanomaterials unique properties, these same properties can potentially cause adverse health effects to workers who may be exposed during work. Dispersed nanoparticles in air can cause adverse health effects to animals not merely due to their chemical properties but due to their size, structure, shape, surface chemistry, solubility, carcinogenicity, reproductive toxicity, mutagenicity, dermal toxicity, and parent material toxicity. Nanoparticles have a greater likelihood of lung deposition and blood absorption than larger particles due to their size. Nanomaterials can also pose physical hazards due to their unusually high reactivity, which makes them useful as catalysts, but has the potential to cause fires and explosions. Characterization of the hazards (and potential for exposures) associated with nanomaterial development and incorporation in other products is an essential step in the development of nanotechnologies. Developing controls for these hazards are equally important. Engineered controls should be integrated into nanomaterial manufacturing process design according to 10CFR851, DOE Policy 456.1, and DOE Notice 456.1 as safety-related hardware or administrative controls for worker safety. Nanomaterial hazards in a nuclear facility must also meet control requirements per DOE standards 3009, 1189, and 1186. Integration of safe designs into manufacturing processes for new applications concurrent with the developing technology is essential for worker safety. This paper presents a discussion of nanotechnology, nanomaterial properties/hazards and controls

Integrated Omics in Systems Biology: The New Frontier for Environmental Biotechnology

OpenAIRE

Hazen, Terry C.

2008-01-01

Environmental biotechnology encompasses a wide range of characterization, monitoring and control for bioenergy and bioremediation technologies that are based on biological processes. Recent breakthroughs in our understanding of biogeochemical processes and genomics are leading to exciting new and cost effective ways to monitor and manipulate the environment and potentially produce bioenergy fuels as we also cleanup the environment. Indeed, our ability to sequence an entire microbial genome in...

Omics in Reproductive Medicine: Application of Novel Technologies to Improve the IVF Success Rate.

Science.gov (United States)

Nerenz, R D

Treatment for many infertile couples often consists of in vitro fertilization (IVF) but an estimated 70% of IVF cycles fail to produce a live birth. In an attempt to improve the live birth rate, the vast majority of IVF cycles performed in the United States involve the transfer of multiple embryos, a practice that increases the risk of multiple gestation pregnancy. This is a concern because multiple gestation pregnancies are associated with an increased incidence of maternal and fetal complications and significant cost associated with the care of preterm infants. As the ideal outcome of each IVF cycle is the birth of a single healthy baby, significant effort has focused on identifying embryos with the greatest developmental potential. To date, selection of euploid embryos using comprehensive chromosome screening (CCS) is the most promising approach while metabolomic and proteomic assessment of spent culture medium have the potential to noninvasively assess embryo viability. Endometrial gene expression profiling may help determine the optimal time to perform embryo transfer. While CCS has been implemented in some clinics, further development and optimization will be required before analysis of spent culture medium and endometrial gene expression profiling make the transition to clinical use. This review will describe efforts to identify embryos with the greatest potential to result in a healthy, live birth, with a particular emphasis on detection of embryo aneuploidy and metabolic profiling of spent embryo culture medium. Assessment of endometrial receptivity to identify the optimal time to perform embryo transfer will also be discussed. © 2016 Elsevier Inc. All rights reserved.

Metabolomics in transfusion medicine.

Science.gov (United States)

Nemkov, Travis; Hansen, Kirk C; Dumont, Larry J; D'Alessandro, Angelo

2016-04-01

Biochemical investigations on the regulatory mechanisms of red blood cell (RBC) and platelet (PLT) metabolism have fostered a century of advances in the field of transfusion medicine. Owing to these advances, storage of RBCs and PLT concentrates has become a lifesaving practice in clinical and military settings. There, however, remains room for improvement, especially with regard to the introduction of novel storage and/or rejuvenation solutions, alternative cell processing strategies (e.g., pathogen inactivation technologies), and quality testing (e.g., evaluation of novel containers with alternative plasticizers). Recent advancements in mass spectrometry-based metabolomics and systems biology, the bioinformatics integration of omics data, promise to speed up the design and testing of innovative storage strategies developed to improve the quality, safety, and effectiveness of blood products. Here we review the currently available metabolomics technologies and briefly describe the routine workflow for transfusion medicine-relevant studies. The goal is to provide transfusion medicine experts with adequate tools to navigate through the otherwise overwhelming amount of metabolomics data burgeoning in the field during the past few years. Descriptive metabolomics data have represented the first step omics researchers have taken into the field of transfusion medicine. However, to up the ante, clinical and omics experts will need to merge their expertise to investigate correlative and mechanistic relationships among metabolic variables and transfusion-relevant variables, such as 24-hour in vivo recovery for transfused RBCs. Integration with systems biology models will potentially allow for in silico prediction of metabolic phenotypes, thus streamlining the design and testing of alternative storage strategies and/or solutions. © 2015 AABB.

Bayesian networks for omics data analysis

NARCIS (Netherlands)

Gavai, A.K.

2009-01-01

This thesis focuses on two aspects of high throughput technologies, i.e. data storage and data analysis, in particular in transcriptomics and metabolomics. Both technologies are part of a research field that is generally called ‘omics’ (or ‘-omics’, with a leading hyphen), which refers to genomics,

Potential Science and Technology Game Changers for the Ground Warfare of 2050: Selected Projections Made in 2017

Science.gov (United States)

2018-02-01

ARL-TR-8283 ● FEB 2018 US Army Research Laboratory Potential Science and Technology Game Changers for the Ground Warfare of 2050...Science and Technology Game Changers for the Ground Warfare of 2050: Selected Projections Made in 2017 by Alexander Kott Office of the Director...Brian Sadler Vehicle Technology Directorate, ARL Ananthram Swami Computational and Information Sciences Directorate, ARL Approved for

Assessment of potential greenhouse gas mitigation of available household solid waste treatment technologies

Directory of Open Access Journals (Sweden)

Hoang Minh Giang

2013-11-01

Full Text Available Current household solid waste treatment practices in most cities in Vietnam caused a great amount of direct greenhouse gas (GHG emissions. Available solid waste treatment technologies should be seriously taken  into consideration as a wedge of GHG mitigation in waste sector base on presently Vietnamese economic conditions. This study aim to evaluate the potential amount of GHG mitigation from current domestic solid waste treatment technologies in Vietnam including landfills and composting from various management scenarios. In oder to use Tier 2 model of IPCC 2006 for GHG estimation from landfills, an analysis on current household solid waste management system of the city was obtained by using material flow analysis approach. A case study in Hanoi, the capital city of Vietnam was carried out in this research. As a result, there was a reduced of over 70% of the amount of CH4 emissions and  up to 53% of total GHG saving (CO2-eq from avoiding organic waste to landfill. In addition, applying an energy recovery from LFG system to available landfills would lead to aproximately 75% of GHG saved compare to current emission of waste sector.Doi: http://dx.doi.org/10.12777/wastech.1.1.10-16Citation: Giang, H.M.,Luong, N.D., and Huong, L.T.M.2013. Assessment of potential greenhouse gas mitigation of available household solid waste treatment technologies. . Waste Technology 1(1:6-9. Doi: http://dx.doi.org/10.12777/wastech.1.1.10-16

Single-cell sequencing in stem cell biology.

Science.gov (United States)

Wen, Lu; Tang, Fuchou

2016-04-15

Cell-to-cell variation and heterogeneity are fundamental and intrinsic characteristics of stem cell populations, but these differences are masked when bulk cells are used for omic analysis. Single-cell sequencing technologies serve as powerful tools to dissect cellular heterogeneity comprehensively and to identify distinct phenotypic cell types, even within a 'homogeneous' stem cell population. These technologies, including single-cell genome, epigenome, and transcriptome sequencing technologies, have been developing rapidly in recent years. The application of these methods to different types of stem cells, including pluripotent stem cells and tissue-specific stem cells, has led to exciting new findings in the stem cell field. In this review, we discuss the recent progress as well as future perspectives in the methodologies and applications of single-cell omic sequencing technologies.

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

An integrated omic analysis of hepatic alteration in medaka fish chronically exposed to cyanotoxins with possible mechanisms of reproductive toxicity.

Science.gov (United States)

Qiao, Qin; Le Manach, Séverine; Huet, Hélène; Duvernois-Berthet, Evelyne; Chaouch, Soraya; Duval, Charlotte; Sotton, Benoit; Ponger, Loïc; Marie, Arul; Mathéron, Lucrèce; Lennon, Sarah; Bolbach, Gérard; Djediat, Chakib; Bernard, Cécile; Edery, Marc; Marie, Benjamin

2016-12-01

Cyanobacterial blooms threaten human health as well as the population of other living organisms in the aquatic environment, particularly due to the production of natural toxic components, the cyanotoxin. So far, the most studied cyanotoxins are microcystins (MCs). In this study, the hepatic alterations at histological, proteome and transcriptome levels were evaluated in female and male medaka fish chronically exposed to 1 and 5 μg L -1 microcystin-LR (MC-LR) and to the extract of MC-producing Microcystis aeruginosa PCC 7820 (5 μg L -1 of equivalent MC-LR) by balneation for 28 days, aiming at enhancing our understanding of the potential reproductive toxicity of cyanotoxins in aquatic vertebrate models. Indeed, both MC and Microcystis extract adversely affect reproductive parameters including fecundity and egg hatchability. The liver of toxin treated female fish present glycogen storage loss and cellular damages. The quantitative proteomics analysis revealed that the quantities of 225 hepatic proteins are dysregulated. In particular, a notable decrease in protein quantities of vitellogenin and choriogenin was observed, which could explain the decrease in reproductive output. Liver transcriptome analysis through Illumina RNA-seq reveals that over 100-400 genes are differentially expressed under 5 μg L -1  MC-LR and Microcystis extract treatments, respectively. Ingenuity pathway analysis of the omic data attests that various metabolic pathways, such as energy production, protein biosynthesis and lipid metabolism, are disturbed by both MC-LR and the Microcystis extract, which could provoke the observed reproductive impairment. The transcriptomics analysis also constitutes the first report of the impairment of circadian rhythm-related gene induced by MCs. This study contributes to a better understanding of the potential consequences of chronic exposure of fish to environmental concentrations of cyanotoxins, suggesting that Microcystis extract could impact a

Novel Materials, Processing, and Device Technologies for Space Exploration with Potential Dual-Use Applications

Science.gov (United States)

Hepp, A. F.; Bailey, S. G.; McNatt, J. S.; Chandrashekhar, M. V. S.; Harris, J. D.; Rusch, A. W.; Nogales, K. A.; Goettsche, K. V.; Hanson, W.; Amos, D.;

LNG - Status in Denmark. Technology and potential. Project report

Energy Technology Data Exchange (ETDEWEB)

Naeslund, M.

2012-05-15

The interest for LNG both on a small and a large scale is increasing worldwide. The experiences and knowledge on LNG is limited in Denmark. The Danish gas companies' Technical Management Group (TCG) has asked for a status report including a technology description and an evaluation of the potential in Denmark. A survey of primarily small-scale LNG technology is done in the report. The focus is motivated by the new areas of gas utilisation that become possible with small-scale LNG. Small-scale LNG in this study is defined as LNG stored and used at the application or in an isolated gas grid. The small-scale use of LNG has today an almost negligible share of the total LNG trade but offers interesting new applications for gas utilisation. LNG on a small scale can be used primarily as: 1) Ship fuel. 2) Truck fuel (heavy duty long distance). 3) Individual users not connected to the natural gas grid. 4) Backup for upgraded biogas to individual users and vehicle fleets. 5) Security of supply or supply enhancement of heavily loaded parts of the gas grid. 6) Small-scale storage and/or peak shaving. All but the first topics are natural uses for the current Danish gas distributors. LNG as ship fuel may engage other specialized LNG companies. The report contains a technical description of the parts in primarily small-scale LNG handling and operation. Liquefaction, transport, storage, engine technologies, gas quality and safety aspects related to LNG are covered. There seem to be two more or less separate paths for LNG in Denmark, onshore and off-shore use. These are not, apparently, sharing their experiences and knowledge. Rules and regulations are also different which may create some problems in the interface, for example ship bunkering. Further studies are suggested in the area of gas quality and engine technologies and adaptation of foreign guidelines for small-scale installations to Danish conditions. These guidelines ought to be based on international standards and

Positive technology–A powerful partnership between positive psychology and interactive technology. A discussion of potential and challenges.

Directory of Open Access Journals (Sweden)

Sarah Diefenbach

2017-11-01

Full Text Available Under the umbrella term "positive computing" concepts of positive psychology are transferred to the domain of human-computer interaction (HCI. In an interdisciplinary community psychologist, computer scientists, designers and others are exploring promising ways how to utilize interactive technology to support wellbeing and human flourishing. Along with this, the recent popularity of smartphone apps aiming at the improvement of health behavior, mindfulness and positive routines, suggests the general acceptance of technology as a facilitator of personal development. Given this, there generally seems a high potential for a technology mediated trigger of positive behavior change, especially in context of positive psychology and resource oriented approaches such as solution-focused coaching. At the same time, there is still a lack of well-founded approaches to design such technology which consider its responsible role as an "interactive coach" and systematically integrate the needed expertise of different disciplines. The present article discusses the general potential and particular challenges to support the goals of positive psychology and human desire for self-improvement through interactive technology and highlights critical steps for a successful partnership between both.

Predictive Technology Management for the Identification of Future Development Trends and the Maximum Achievable Potential Based on a Quantitative Analysis

Directory of Open Access Journals (Sweden)

Michael Fries

2017-07-01

Full Text Available A company’s ability to find the most profitable technology is based on a precise forecast of achievement potential. Technology Management (TM uses forecasting models to analyse future potentials, e.g. the Gartner Hype Cycle, Arthur D. Little’s technology lifecycle or McKinsey’s S-curve model. All these methods are useful for qualitative analysis in the planning of strategic research and development (R&D expenses. In a new approach, exponential and logistic growth functions are used to identify and quantify characteristic stages of technology development. Innovations from electrical, mechanical and computer engineering are observed and projected until the year 2025. Datasets from different industry sectors are analysed, as the number of active Facebook users worldwide, the tensile yield point of flat bar steel, the number of transistors per unit area on integrated circuits, the fuel efficiency per dimension of passenger cars, and the energy density of Lithium-Ion cells. Results show the period of performance doubling and the forecast for the end of the technological achievement potential. The methodology can help to answer key entrepreneurial questions such as the search for alternatives to applied technologies, as well as identifying the risk of substitution technology.

Opportunities for Cancer-relevant Innovative Technologies with Transformative Potential | Office of Cancer Clinical Proteomics Research

Science.gov (United States)

The National Cancer Institute (NCI) is seeking input from the community on identifying priorities with regards to supporting innovative technology development for cancer-relevant research. While the NCI provides support for technology development through a variety of mechanisms, it is important to understand whether or not these are sufficient for catalyzing and supporting the development of tools with significant potential for advancing important fields of cancer research or clinical care.

Nutrigenomics: the cutting edge and Asian perspectives.

Science.gov (United States)

Kato, Hisanori

2008-01-01

One of the two major goals of nutrigenomics is to make full use of genomic information to reveal how genetic variations affect nutrients and other food factors and thereby realize tailor-made nutrition (nutrigenetics). The other major goal of nutrigenomics is to comprehensively understand the response of the body to diets and food factors through various 'omics' technologies such as transcriptomics, proteomics, and metabolomics. The most successfully exploited technology to date is transcriptome analysis, due mainly to its efficiency and high-throughput feature. This technology has already provided a substantial amount of data on, for instance, the novel function of food factors, the unknown mechanism of the effect of nutrients, and even safety issues of foods. The nutrigenomics database that we have created now holds the publication data of several hundred of such 'omics' studies. Furthermore, the transcriptomics approach is being applied to food safety issues. For ex-ample, the data we have obtained thus far suggest that this new technology will facilitate the safety evaluation of newly developed foods and will help clarify the mechanism of toxic effects resulting from the excessive intake of a nutrient. The 'omics' data accumulated by our group and others strongly support the promise of the systems biology approach to food and nutrition science.

Report to Congress on the Potential Environmental Effects of Marine and Hydrokinetic Energy Technologies

Energy Technology Data Exchange (ETDEWEB)

Cada, Glenn [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2009-12-01

This report focuses on potential impacts of marine and hydrokinetic technologies to aquatic environments (i.e. rivers, estuaries, and oceans), fish and fish habitats, ecological relationships, and other marine and freshwater aquatic resources. The report does not address impacts to terrestrial ecosystems and organisms that are common to other electricity-generating technologies (e.g., construction and maintenance of transmission lines) or possible effects on the human environment, including: human use conflicts, aesthetics, viewsheds, noise in the terrestrial environment, light, recreation, transportation, navigation, cultural resources, socioeconomic impacts.

Potential of impulse drying technology for molded pulp products manufacture

DEFF Research Database (Denmark)

Didone, Mattia; Tosello, Guido

2016-01-01

The vision of the Green Fiber Bottle (GFB) project is to develop a paper bottle for beer, which will be both recyclable and biodegradable. The early prototypes of the bottle are very promising but there are huge technical and scientific challenges ahead to mature the production technology....... The possibility of applying the concept of impulse drying during the drying stage is suggested. This would give benefits in terms of productivity and it would also reduce energy consumption.With the aim of understanding and controlling the impulse drying phenomena, a simplified approach is proposed. Finally......, a potential design for a testing equipment is described....

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.

The potential use of mobile technology: enhancing accessibility and communication in a blended learning course

OpenAIRE

Mayisela, Tabisa

2013-01-01

Mobile technology is increasingly being used to support blended learning beyond computer centres. It has been considered as a potential solution to the problem of a shortage of computers for accessing online learning materials (courseware) in a blended learning course. The purpose of the study was to establish how the use of mobile technology could enhance accessibility and communication in a blended learning course. Data were solicitedfrom a purposive convenience sample of 36 students engage...

Transcriptome data modeling for targeted plant metabolic engineering.

Science.gov (United States)

Yonekura-Sakakibara, Keiko; Fukushima, Atsushi; Saito, Kazuki

2013-04-01

The massive data generated by omics technologies require the power of bioinformatics, especially network analysis, for data mining and doing data-driven biology. Gene coexpression analysis, a network approach based on comprehensive gene expression data using microarrays, is becoming a standard tool for predicting gene function and elucidating the relationship between metabolic pathways. Differential and comparative gene coexpression analyses suggest a change in coexpression relationships and regulators controlling common and/or specific biological processes. In conjunction with the newly emerging genome editing technology, network analysis integrated with other omics data should pave the way for robust and practical plant metabolic engineering. Copyright © 2012 Elsevier Ltd. All rights reserved.

A review of the available technologies for sealing a potential underground nuclear waste repository at Yucca Mountain, Nevada

International Nuclear Information System (INIS)

Fernandez, J.A.; Richardson, A.M.

1994-11-01

The purpose of this report is to assess the availability of technologies to seal underground openings. The technologies are needed to seal the potential high-level radioactive waste repository at Yucca Mountain. Technologies are evaluated for three basic categories of seal components: backfill (general fill and graded fill), bulkheads, and grout curtains. Not only is placement of seal components assessed, but also preconditioning of the placement area and seal component durability. The approach taken was: First, review selected sealing case histories (literature searches and site visits) from the mining, civil, and defense industries; second, determine whether reasonably available technologies to seal the potential repository exist; and finally, identify deficiencies in existing technologies. It is concluded that reasonably available technologies do exist to place backfill, bulkheads, and grout curtains. Technologies also exist to precondition areas where seal components are to be placed. However, if final performance requirements are stringent for these engineered structures, some existing technologies may need to be developed. Deficiencies currently do exist in technologies that demonstrate the long-term durability and performance of seal components. Case histories do not currently exist that demonstrate the placement of seal components in greatly elevated thermal and high-radiation environments and in areas where ground support (rock bolts and concrete liners) has been removed. The as-placed, in situ material properties for sealing materials appropriate to Yucca Mountain are not available

Potential of Wolfram technologies in construction and research of econometric models

Directory of Open Access Journals (Sweden)

Dmitry A. Vlasov

2017-12-01

Full Text Available In the center of attention of article didactic, applied and research potentials of technologies of the modern knowledge base and a set of computing algorithms Wolfram in creation and a research of econometric models. Econometric models and methods traditionally play a special role in applied mathematical training of students of an economic bachelor degree in Plekhanov Russian University of Economics. Within this article experience of forming of content of applied mathematical training of future bachelor of economy and methodical features of use of information technologies in the course of econometric modeling of social and economic situations and teaching subject matters of «The econometrician (basic level» for students of an economic bachelor degree and «The econometrician (advanced level» for students of an economic magistracy is provided. The allocated sixteen tools fully allow to focus attention to development of innovative components of professional competence of future bachelors of economy.

The role and potential of information technology in agricultural improvement

Directory of Open Access Journals (Sweden)

Milovanović Slavoljub

2014-01-01

Full Text Available The agro-industrial sector in developing countriesis faced with challenges, such as requirement for increase of food production and yield and creation of opportunity for employment of rural and poor population. In addition, the agricultural sector is influenced by global factors and fast changes. These facts indicate that there is great need for information and information technologies (IT, which can be used to cope with the challenges and changes and to improve agricultural production and marketing. However, the potential of IT is not fully utilized in agriculture. Implementation of IT in agricultural sector and rural areas is relatively slow in comparison to the other sectors of the economy where contemporary IT has been implemented at high speed. The aim of the paper is to analyze role, potential and contribution of IT in agribusiness and to explain opportunities for use of IT in many fields of agricultural sector. Our findings are based on economic theory and available literature, and they suggest that IT has great potential for supporting farmers and the other stakeholders in improvement of efficiency, effectiveness and productivity of agriculture. However, the stakeholders have to cope with many limitations and problems in IT implementation and use.

Systems biology of yeast: enabling technology for development of cell factories for production of advanced biofuels.

Science.gov (United States)

de Jong, Bouke; Siewers, Verena; Nielsen, Jens

2012-08-01

Transportation fuels will gradually shift from oil based fuels towards alternative fuel resources like biofuels. Current bioethanol and biodiesel can, however, not cover the increasing demand for biofuels and there is therefore a need for advanced biofuels with superior fuel properties. Novel cell factories will provide a production platform for advanced biofuels. However, deep cellular understanding is required for improvement of current biofuel cell factories. Fast screening and analysis (-omics) methods and metabolome-wide mathematical models are promising techniques. An integrated systems approach of these techniques drives diversity and quantity of several new biofuel compounds. This review will cover the recent technological developments that support improvement of the advanced biofuels 1-butanol, biodiesels and jetfuels. Copyright © 2011 Elsevier Ltd. All rights reserved.

Techno-economic viability assessments of greener propulsion technology under potential environmental regulatory policy scenarios

International Nuclear Information System (INIS)

Nalianda, D.K.; Kyprianidis, K.G.; Sethi, V.; Singh, R.

2015-01-01

Highlights: • An advanced method is presented for techno-economic assessment under potential environmental regulatory policy scenarios. • The viability of the contra-rotating open rotor concept is investigated under various environmental policies. • CO_2 taxation is needed to drive the aerospace industry towards greener solutions. - Abstract: Sustainability of the aviation industry, as any other industry, depends on the elasticity of demand for the product and profitability through minimising operating costs. Of paramount importance is assessing and understanding the interdependency and effects of environmentally optimised solutions and emission mitigation policies. This paper describes the development and application of assessment methodologies to better understand the effects of environmental taxation/energy policies aimed at environmental pollution reduction and the future potential economic impact they may have on the adaptation of “greener” novel technologies. These studies are undertaken using a Techno-economic Environmental Risk Assessment approach. The methodology demonstrated allows the assessment of the economic viability of new technologies compared to conventional technologies, for various CO_2 emission taxation and fuel price scenarios. It considers relative increases in acquisition price and maintenance costs. A study undertaken as a ‘proof of concept’ compares a Counter Rotating Open Rotor aircraft with a conventional aircraft for short range operations. It indicates that at current fuel price and with no carbon taxation, a highly fuel efficient technology, such as the one considered, could be rendered economically unviable. The work goes on to demonstrate that in comparison to the conventional aircraft, any economic benefits that may be accrued from improvement in fuel consumption through such a technology, may well be negated through increases in acquisition price and maintenance costs. The work further demonstrates that if policy

Health Educational Potentials of Technologies

DEFF Research Database (Denmark)

Magnussen, Rikke; Aagaard-Hansen, Jens

2012-01-01

The field of health promotion technology has been in an exponential growth in recent years and smart phone applications, exer-games and self-monitoring devices has become part of fitness activities and health education. In this work-in-progress-paper theoretical perspectives for categorising...

LCOE reduction potential of parabolic trough and solar tower CSP technology until 2025

Science.gov (United States)

Dieckmann, Simon; Dersch, Jürgen; Giuliano, Stefano; Puppe, Michael; Lüpfert, Eckhard; Hennecke, Klaus; Pitz-Paal, Robert; Taylor, Michael; Ralon, Pablo

2017-06-01

Concentrating Solar Power (CSP), with an installed capacity of 4.9 GW by 2015, is a young technology compared to other renewable power generation technologies. A limited number of plants and installed capacity in a small challenging market environment make reliable and transparent cost data for CSP difficult to obtain. The International Renewable Energy Agency (IRENA) and the DLR German Aerospace Center gathered and evaluated available cost data from various sources for this publication in order to yield transparent, reliable and up-to-date cost data for a set of reference parabolic trough and solar tower plants in the year 2015 [1]. Each component of the power plant is analyzed for future technical innovations and cost reduction potential based on current R&D activities, ongoing commercial developments and growth in market scale. The derived levelized cost of electricity (LCOE) for 2015 and 2025 are finally contrasted with published power purchase agreements (PPA) of the NOOR II+III power plants in Morocco. At 7.5% weighted average cost of capital (WACC) and 25 years economic life time, the levelized costs of electricity for plants with 7.5 (trough) respectively 9 (tower) full-load hours thermal storage capacity decrease from 14-15 -ct/kWh today to 9-10 -ct/kWh by 2025 for both technologies at direct normal irradiation of 2500 kWh/(m².a). The capacity factor increases from 41.1% to 44.6% for troughs and from 45.5% to 49.0% for towers. Financing conditions are a major cost driver and offer potential for further cost reduction with the maturity of the technology and low interest rates (6-7 - ct/kWh for 2% WACC at 2500 kWh/(m2.a) in 2025).

Assessment of Suitable Areas for Home Gardens for Irrigation Potential, Water Availability, and Water-Lifting Technologies

Directory of Open Access Journals (Sweden)

Tewodros Assefa

2018-04-01

Full Text Available The study was conducted in Lake Tana Basin of Ethiopia to assess potentially irrigable areas for home gardens, water availability, and feasibility of water-lifting technologies. A GIS-based Multi-Criteria Evaluation (MCE technique was applied to access the potential of surface and groundwater sources for irrigation. The factors affecting irrigation practice were identified and feasibility of water-lifting technologies was evaluated. Pairwise method and expert’s opinion were used to assign weights for each factor. The result showed that about 345,000 ha and 135,000 ha of land were found suitable for irrigation from the surface and groundwater sources, respectively. The rivers could address about 1–1.2% of the irrigable land during dry season without water storage structure whereas groundwater could address about 2.2–2.4% of the irrigable land, both using conventional irrigation techniques. If the seven major dams within the basin were considered, surface water potential would be increased and satisfy about 21% of the irrigable land. If rainwater harvesting techniques were used, about 76% of the basin would be suitable for irrigation. The potential of surface and groundwater was evaluated with respect to water requirements of dominant crops in the region. On the other hand, rope pump and deep well piston hand pump were found with relatively the most (26% and the least (9% applicable low-cost water-lifting technologies in the basin.

[Current status and potential perspectives in classical radiotherapy technology].

Science.gov (United States)

Dabić-Stanković, Kata M; Stanković, Jovan B; Radosević-Jelić, Ljiljana M

2004-01-01

After purchase of radiotherapy equipment in 2003, classic radiation therapy in Serbia will reach the highest world level. In order to define the highest standards in radiation technology, we analyzed the current status and potential perspectives of radiation therapy. An analysis of present situation in the USA, assumed as the most developed in the world, was done. Available data, collected in the last 3 years (equipment assortment, therapy modalities, workload and manpower) for 284 radiotherapy centers, out of potential 2050, were analyzed. Results were presented as crude percentage and matched to point current status. The analysis showed that CLINAC accelerators are the most popular (82.7%), as well as, ADAC (43.7%) and Focus (CMS) (27.4%) systems for therapy planning. Movement towards virtual simulation is evident (59.3%), although classic "simulation" is not fully eliminated from the radiotherapy chain. The most popular brachytherapy afterloader is Microselectron HDR (71%). About 64.4% centers use IMPAC communication/verification/record system that seems more open than Varis. All centers practice modern radiotherapy modalities and techniques (CPRT, IMRT, SRS/SRT, TBI, IORT, IVBHRT, HDR BHRT, etc.). CT and MRI availability is out of question, but PET is available in 3% of centers, however this percentage is rapidly growing. Up to 350 new patients per year are treated by one accelerator (about 35 pts. a day). Centers are relatively small and utilize 2-3 accelerators on average. Average FTE staffing norm is 4 radiation oncologists, 2-3 medical radiotherapy physicists, about 3 certified medical dosimetrists and about 6 radiotherapy technologists. In the past 5 years relative stagnation in classic radiotherapy has been observed. In spite of substantial investments in technology and consequent improvements, as well as wide introduction of computers in radiotherapy, radiotherapy results have not changed significantly. Vendor developement strategies do not point that

Zero emissions trucks. An overview of state-of-the-art technologies and their potential

Energy Technology Data Exchange (ETDEWEB)

Den Boer, E.; Aarnink, S. [CE Delft, Delft (Netherlands); Kleiner, F.; Pagenkopf, J. [German Aerospace Center DLR, Cologne (Germany)

2013-07-15

The study by CE Delft and the German Aerospace Center (DLR), commissioned by the International Council on Clean Transportation (ICCT), surveys the technology potential for zero-emission road freight transport in the EU. For short distance transport, battery electric technology is feasible, as distribution trucks have lower range requirements and recharging can occur at scheduled downtimes (e.g. overnight). For long haul applications, battery electric vehicles coupled with overhead wires (catenary) or in-road charging (dynamic) infrastructure are possible, as well as fuel cell drivelines. The cost differential between conventional and zero emission HDVs will diminish over the next 10-15 years, as fuel savings offset other costs. If zero-emission technologies are introduced on a large scale in the onroad freight transport sector beginning in 2020, the total end-user costs will not significantly increase. The total cost of ownership within this study do not consider required infrastructure investments. All zero emission technologies require major infrastructure investments, whether hydrogen refuelling stations, in-road inductive charging, or other systems. Broad policy support is needed to encourage the development and evaluation of various technology options. Over time, the policy focus must shift from stimulating innovation and technology adoption to regulation, if it is to spur a successful transformation of the truck market.

Emerging technologies, recent developments, and novel applications for drug metabolite identification.

Science.gov (United States)

Lu, Wenjie; Xu, Youzhi; Zhao, Yinglan; Cen, Xiaobo

2014-01-01

Drug metabolite identification and metabolic characteristics analysis play a crucial role in new drug research and development, because they can lead to varied efficacy, severe adverse reactions, and even toxicity. Classical methodologies for metabolite identification have mainly been based on mass spectrometry (MS) coupled with gas chromatography (GC) or liquid chromatography (LC), and some other techniques are used as complementary approaches, such as nuclear magnetic resonance (NMR). Over the past decade, more and more newly emerging techniques or technologies have been applied to metabolite identification, and are making the procedure easier and more robust, such as LC-NMR-MS, ion mobility MS, ambient ionization techniques, and imaging MS. A novel application of drug metabolite identification based on "omics" known as pharmacometabonomics is discussed, which is an interdisciplinary field that combines pre-dose metabolite profiling and chemometrics methods for data analysis and modeling, aiming to predict the responses of individuals to drugs.

The potential risks from metals bottlenecks to the deployment of Strategic Energy Technologies

International Nuclear Information System (INIS)

Moss, R.L.; Tzimas, E.; Kara, H.; Willis, P.; Kooroshy, J.

2013-01-01

This paper examines the use of materials, in particular metals, in six low-carbon energy technologies of the European Union's Strategic Energy Technology Plan (SET-Plan), namely nuclear, solar, wind, bioenergy, carbon capture and storage and electricity grids. The projected average annual demand for metals in the SET-Plan technologies for the decades up to 2020 and 2030 is compared to the known global production volume in 2010. From an initial inventory of over 50 metals, 14 metals were identified that will require 1% or more of the 2010 world supply per annum between 2020 and 2030. These 14 metals are cadmium, dysprosium, gallium, hafnium, indium, molybdenum, neodymium, nickel, niobium, selenium, silver, tellurium, tin and vanadium. These metals were examined further by analysing the effect of market and geo-political factors of supply and demand, which highlighted five metals to represent a high risk to large-scale technology deployment, namely: neodymium, dysprosium, indium, tellurium and gallium. The five metals were further analysed with respect to the wind and solar sectors, showing that the demand of these metals could increase significantly depending on future sub-technology choices. Mitigation strategies to alleviate potential shortages are also discussed, e.g. extending primary output; re-use, re-cycling and waste reduction; and substitution. - Highlights: ► Over 50 metals and their usage in six low-carbon energy technologies are analysed. ► 14 metals are identified that will require 1% or more of the 2010 world supply per annum. ► The 14 metals are further examined with respect to market and geo-political factors. ► 5 metals Nd, Dy, In, Te and Ga are a high risk to large-scale technology deployment. ► Demand for the 5 metals increases for sub-technology choices in PV and wind energy

Process Heat Generation Potential from Solar Concentration Technologies in Latin America: The Case of Argentina

Directory of Open Access Journals (Sweden)

Isidoro Lillo

2017-03-01

Full Text Available This paper evaluates the potential of solar concentration technologies—compound parabolic collector (CPC, linear Fresnel collector (LFC and parabolic trough collector (PTC—as an alternative to conventional sources of energy for industrial processes in Latin America, where high levels of solar radiation and isolated areas without energy supply exist. The analysis is addressed from energy, economic and environmental perspective. A specific application for Argentina in which fourteen locations are analyzed is considered. Results show that solar concentration technologies can be an economically and environmentally viable alternative. Levelized cost of energy (LCOE ranges between 2.5 and 16.9 c€/kWh/m2 and greenhouse gas (GHG emissions avoided range between 33 and 348 kgCO2/(m2·year. CPC technology stands out as the most recommendable technology when the working fluid temperature ranges from 373 K to 423 K. As the working fluid temperature increases the differences between the LCOE values of the CPC and LFC technologies decrease. When 523 K is reached LFC technology is the one which presents the lowest LCOE values for all analyzed sites, while the LCOE values of PTC technology are close to CPC technology values. Results show that solar concentration technologies have reached economic and environmental competitiveness levels under certain scenarios, mainly linked to solar resource available, thermal level requirements and solar technology cost.

Multi-omics Analysis Sheds Light on the Evolution and the Intracellular Lifestyle Strategies of Spotted Fever Group Rickettsia spp.

Science.gov (United States)

El Karkouri, Khalid; Kowalczewska, Malgorzata; Armstrong, Nicholas; Azza, Said; Fournier, Pierre-Edouard; Raoult, Didier

2017-01-01

Arthropod-borne Rickettsia species are obligate intracellular bacteria which are pathogenic for humans. Within this genus, Rickettsia slovaca and Rickettsia conorii cause frequent and potentially severe infections, whereas Rickettsia raoultii and Rickettsia massiliae cause rare and milder infections. All four species belong to spotted fever group (SFG) rickettsiae. However, R. slovaca and R. raoultii cause scalp eschar and neck lymphadenopathy (SENLAT) and are mainly associated with Dermacentor ticks, whereas the other two species cause Mediterranean spotted fever (MSF) and are mainly transmitted by Rhipicephalus ticks. To identify the potential genes and protein profiles and to understand the evolutionary processes that could, comprehensively, relate to the differences in virulence and pathogenicity observed between these four species, we compared their genomes and proteomes. The virulent and milder agents displayed divergent phylogenomic evolution in two major clades, whereas either SENLAT or MSF disease suggests a discrete convergent evolution of one virulent and one milder agent, despite their distant genetic relatedness. Moreover, the two virulent species underwent strong reductive genomic evolution and protein structural variations, as well as a probable loss of plasmid(s), compared to the two milder species. However, an abundance of mobilome genes was observed only in the less pathogenic species. After infecting Xenopus laevis cells, the virulent agents displayed less up-regulated than down-regulated proteins, as well as less number of identified core proteins. Furthermore, their similar and distinct protein profiles did not contain some genes (e.g., omp A/B and rick A) known to be related to rickettsial adhesion, motility and/or virulence, but may include other putative virulence-, antivirulence-, and/or disease-related proteins. The identified evolutionary forces herein may have a strong impact on intracellular expressions and strategies in these

Multi-omics Analysis Sheds Light on the Evolution and the Intracellular Lifestyle Strategies of Spotted Fever Group Rickettsia spp.

Directory of Open Access Journals (Sweden)

Khalid El Karkouri

2017-07-01

Full Text Available Arthropod-borne Rickettsia species are obligate intracellular bacteria which are pathogenic for humans. Within this genus, Rickettsia slovaca and Rickettsia conorii cause frequent and potentially severe infections, whereas Rickettsia raoultii and Rickettsia massiliae cause rare and milder infections. All four species belong to spotted fever group (SFG rickettsiae. However, R. slovaca and R. raoultii cause scalp eschar and neck lymphadenopathy (SENLAT and are mainly associated with Dermacentor ticks, whereas the other two species cause Mediterranean spotted fever (MSF and are mainly transmitted by Rhipicephalus ticks. To identify the potential genes and protein profiles and to understand the evolutionary processes that could, comprehensively, relate to the differences in virulence and pathogenicity observed between these four species, we compared their genomes and proteomes. The virulent and milder agents displayed divergent phylogenomic evolution in two major clades, whereas either SENLAT or MSF disease suggests a discrete convergent evolution of one virulent and one milder agent, despite their distant genetic relatedness. Moreover, the two virulent species underwent strong reductive genomic evolution and protein structural variations, as well as a probable loss of plasmid(s, compared to the two milder species. However, an abundance of mobilome genes was observed only in the less pathogenic species. After infecting Xenopus laevis cells, the virulent agents displayed less up-regulated than down-regulated proteins, as well as less number of identified core proteins. Furthermore, their similar and distinct protein profiles did not contain some genes (e.g., ompA/B and rickA known to be related to rickettsial adhesion, motility and/or virulence, but may include other putative virulence-, antivirulence-, and/or disease-related proteins. The identified evolutionary forces herein may have a strong impact on intracellular expressions and strategies in

Multi-omics Analysis Sheds Light on the Evolution and the Intracellular Lifestyle Strategies of Spotted Fever Group Rickettsia spp.

Science.gov (United States)

El Karkouri, Khalid; Kowalczewska, Malgorzata; Armstrong, Nicholas; Azza, Said; Fournier, Pierre-Edouard; Raoult, Didier

2017-01-01

Arthropod-borne Rickettsia species are obligate intracellular bacteria which are pathogenic for humans. Within this genus, Rickettsia slovaca and Rickettsia conorii cause frequent and potentially severe infections, whereas Rickettsia raoultii and Rickettsia massiliae cause rare and milder infections. All four species belong to spotted fever group (SFG) rickettsiae. However, R. slovaca and R. raoultii cause scalp eschar and neck lymphadenopathy (SENLAT) and are mainly associated with Dermacentor ticks, whereas the other two species cause Mediterranean spotted fever (MSF) and are mainly transmitted by Rhipicephalus ticks. To identify the potential genes and protein profiles and to understand the evolutionary processes that could, comprehensively, relate to the differences in virulence and pathogenicity observed between these four species, we compared their genomes and proteomes. The virulent and milder agents displayed divergent phylogenomic evolution in two major clades, whereas either SENLAT or MSF disease suggests a discrete convergent evolution of one virulent and one milder agent, despite their distant genetic relatedness. Moreover, the two virulent species underwent strong reductive genomic evolution and protein structural variations, as well as a probable loss of plasmid(s), compared to the two milder species. However, an abundance of mobilome genes was observed only in the less pathogenic species. After infecting Xenopus laevis cells, the virulent agents displayed less up-regulated than down-regulated proteins, as well as less number of identified core proteins. Furthermore, their similar and distinct protein profiles did not contain some genes (e.g., ompA/B and rickA) known to be related to rickettsial adhesion, motility and/or virulence, but may include other putative virulence-, antivirulence-, and/or disease-related proteins. The identified evolutionary forces herein may have a strong impact on intracellular expressions and strategies in these rickettsiae

Potential of the tractor-trailer and container segments as entry markets for a proposed refrigeration technology

Energy Technology Data Exchange (ETDEWEB)

Smith, S.A.; Davis, L.J.; Garrett, B.A.

1987-05-01

The refrigerated trailer and container segments of the transportation industry are evaluated as potential entry markets for a proposed absorption refrigeration technology. To perform this analysis the existing transportation refrigeration industry is characterized; this includes a description of the current refrigeration technology, rating systems, equipment manufacturers, maintenance requirements, and sales trends. This information indicates that the current transportation refrigeration industry is composed of two major competitors, Thermo King and Carrier. In addition, it has low profit potential, some barriers to entry and low growth potential. Data are also presented that characterize the transportation refrigeration consumers, specifically, major groups, market segmentation, consumer decision process, and buying criteria. This consumer information indicates that the majority of refrigerated trailer consumers are private carriers, and that the majority of refrigerated container consumers are shipping companies. Also, these consumers are primarily interested in buying reliable equipment at a low price, and are quite satisfied with existing refrigeration equipment.

The potential environmental gains from recycling waste plastics: simulation of transferring recycling and recovery technologies to Shenyang, China.

Science.gov (United States)

Chen, Xudong; Xi, Fengming; Geng, Yong; Fujita, Tsuyoshi

2011-01-01

With the increasing attention on developing a low-carbon economy, it is necessary to seek appropriate ways on reducing greenhouse gas (GHG) emissions through innovative municipal solid waste management (MSWM), such as urban symbiosis. However, quantitative assessments on the environmental benefits of urban symbiosis, especially in developing countries, are limited because only a limited number of planned synergistic activities have been successful and it is difficult to acquire detailed inventory data from private companies. This paper modifies and applies a two-step simulation system and used it to assess the potential environmental benefits, including the reduction of GHG emissions and saving of fossil fuels, by employing various Japanese plastics recycling/energy-recovery technologies in Shenyang, China. The results showed that among various recycling/energy-recovery technologies, the mechanical waste plastics recycling technology, which produces concrete formwork boards (NF boards), has the greatest potential in terms of reducing GHG emissions (1.66 kg CO(2)e/kg plastics), whereas the technology for the production of refuse plastic fuel (RPF) has the greatest potential on saving fossil fuel consumption (0.77 kg ce/kg-plastics). Additional benefits can be gained by applying combined technologies that cascade the utilization of waste plastics. Moreover, the development of clean energy in conjunction with the promotion of new waste plastics recycling programs could contribute to additional reductions in GHG emissions and fossil fuel consumption. Copyright © 2010 Elsevier Ltd. All rights reserved.

The potential relevance of cognitive neuroscience for the development and use of technology-enhanced learning

NARCIS (Netherlands)

Howard-Jones, Paul; Ott, Michela; van Leeuwen, Theo; De Smedt, Bert

2015-01-01

There is increasing interest in the application of cognitive neuroscience in educational thinking and practice, and here we review findings from neuroscience that demonstrate its potential relevance to technology-enhanced learning (TEL). First, we identify some of the issues in integrating

Reducing automotive emissions—The potentials of combustion engine technologies and the power of policy

International Nuclear Information System (INIS)

Berggren, Christian; Magnusson, Thomas

2012-01-01

Reducing transport emissions, in particular vehicular emissions, is a key element for mitigating the risks of climate change. In much of the academic and public discourse the focus has been on alternative vehicle technologies and fuels (e.g. electric cars, fuel cells and hydrogen), whereas vehicles based on internal combustion engines have been perceived as close to their development limits. This paper offers a different perspective by demonstrating the accelerated improvement processes taking place in established combustion technologies as a result of a new competition between manufacturers and technologies, encouraged both by more stringent EU legislation and new CAFE levels in the US. The short-term perspective is complemented by an analysis of future improvement potentials in internal combustion technologies, which may be realized if efficient regulation is in place. Based on a comparison of four different regulatory approaches, the paper identifies the need for a long-term technology-neutral framework with stepwise increasing stringencies, arguing that this will encourage continual innovation and diffusion in the most effective way. - Highlights: ► From 1990 to 2008, CO 2 emissions from road transportation in the EU increased by 21%. ► Alternative vehicles are important, but internal combustion engines (ICE) will remain dominant. ► The paper shows how competition and new regulation accelerate the improvement of ICE-vehicles. ► The key factor for long-term emissions reduction is appropriate regulation, not technology. ► Most effective is a technology-neutral framework with stepwise increasing stringencies.

Energy conservation potential of surface modification technologies

Energy Technology Data Exchange (ETDEWEB)

Le, H.K.; Horne, D.M.; Silberglitt, R.S.

1985-09-01

This report assesses the energy conservation impact of surface modification technologies on the metalworking industries. The energy conservation impact of surface modification technologies on the metalworking industries is assessed by estimating their friction and wear tribological sinks and the subsequent reduction in these sinks when surface modified tools are used. Ion implantation, coatings, and laser and electron beam surface modifications are considered.

Cellulosic ethanol. Potential, technology and development status

Energy Technology Data Exchange (ETDEWEB)

Rarbach, M. [Sued-Chemie AG, Muenchen (Germany)

2012-07-01

In times of rising oil prices and a growing energy demand, sustainable alternative energy sources are needed. Cellulosic ethanol is a sustainable biofuel, made from lignocellulosic feedstock such as agricultural residues (corn stover, cereal straw, bagasse) or dedicated energy crops. Its production is almost carbon neutral, doesn't compete with food or feed production and induces no land use changes. It constitutes a new energy source using an already existing renewable feedstock without needing any further production capacity and can thus play a major role on the way to more sustainability in transport and the chemical industry and reducing the dependence on the import of fossil resources. The potential for cellulosic ethanol is huge: In the US, the annual production of agricultural residues (cereal straw and corn stover) reached almost 384 million tons in 2009 and Brazil alone produced more than 670 million tons of sugar cane in 2009 yielding more than 100 million tons of bagasse (dry basis). And alone in the European Union, almost 300 million tons of crop straw are produced annually. The last years have seen success in the development and deployment in the field of cellulosic ethanol production. The main challenge thereby remains to demonstrate that the technology is economically feasible for the up-scaling to industrial scale. Clariant has developed the sunliquid {sup registered} process, a proprietary cellulosic ethanol technology that reaches highest greenhouse gas (GHG) emission savings while cutting production costs to a minimum. The sunliquid {sup registered} process for cellulosic ethanol matches the ambitious targets for economically and ecologically sustainable production and greenhouse gas reduction. It was developed using an integrated design concept. Highly optimized, feedstock and process specific biocatalysts and microorganisms ensure a highly efficient process with improved yields and feedstock-driven production costs. Integrated, on

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.

The Potential of RFID Technology in the Textile and Clothing Industry: Opportunities, Requirements and Challenges

Science.gov (United States)

Legnani, Elena; Cavalieri, Sergio; Pinto, Roberto; Dotti, Stefano

In the current competitive environment, companies need to extensively exploit the use of advanced technologies in order to develop a sustainable advantage, enhance their operational efficiency and better serve customers. In this context, RFID technology has emerged as a valid support for the company progress and its value is becoming more and more apparent. In particular, the textile and clothing industry, characterised by short life-cycles , quick response production , fast distribution, erratic customer preferences and impulsive purchasing, is one of the sectors which can extensively benefit from the RFID technology. However, actual applications are still very limited, especially in the upstream side of the supply network. This chapter provides an insight into the main benefits and potentials of this technology and highlights the main issues which are currently inhibiting its large scale development in the textile and clothing industry. The experience of two industry-academia projects and the relative fallouts are reported.

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

Biofuels and Biotechnology

Energy Technology Data Exchange (ETDEWEB)

Mielenz, Jonathan R [ORNL

2009-01-01

The world obtains 86% of its energy from fossil fuels, 40% from petroleum, a majority of which goes to the transportation sector (www.IEA.gov). Well-recognized alternatives are fuels derived from renewable sources known as biofuels. There are a number of biofuels useful for transportation fuels, which include ethanol, biobutanol, mixed alcohols, biodiesel, and hydrogen. These biofuels are produced from biologically derived feedstock, almost exclusively being plant materials, either food or feed sources or inedible plant material called biomass. This chapter will discuss technologies for production of liquid transportation biofuels from renewable feedstocks, but hydrogen will not be included, as the production technology and infrastructure are not near term. In addition, a specific emphasis will be placed upon the research opportunities and potential for application of system biology tools to dissect and understand the biological processes central to production of these biofuels from biomass and biological materials. There are a number of technologies for production of each of these biofuels that range from fully mature processes such as grain-derived ethanol, emerging technology of ethanol form cellulose derived ethanol and immature processes such thermochemical conversion technologies and production of hydrogen all produced from renewable biological feedstocks. Conversion of biomass by various thermochemical and combustion technologies to produce thermochemical biodiesel or steam and electricity provide growing sources of bioenergy. However, these technologies are outside of the scope of this chapter, as is the use of biological processing for upgrading and conversion of fossil fuels. Therefore, this chapter will focus on the current status of production of biofuels produced from biological-derived feedstocks using biological processes. Regardless of the status of development of the biological process for production of the biofuels, each process can benefit from

Healthcare Databases in Thailand and Japan: Potential Sources for Health Technology Assessment Research.

Directory of Open Access Journals (Sweden)

Surasak Saokaew

Full Text Available Health technology assessment (HTA has been continuously used for value-based healthcare decisions over the last decade. Healthcare databases represent an important source of information for HTA, which has seen a surge in use in Western countries. Although HTA agencies have been established in Asia-Pacific region, application and understanding of healthcare databases for HTA is rather limited. Thus, we reviewed existing databases to assess their potential for HTA in Thailand where HTA has been used officially and Japan where HTA is going to be officially introduced.Existing healthcare databases in Thailand and Japan were compiled and reviewed. Databases' characteristics e.g. name of database, host, scope/objective, time/sample size, design, data collection method, population/sample, and variables were described. Databases were assessed for its potential HTA use in terms of safety/efficacy/effectiveness, social/ethical, organization/professional, economic, and epidemiological domains. Request route for each database was also provided.Forty databases- 20 from Thailand and 20 from Japan-were included. These comprised of national censuses, surveys, registries, administrative data, and claimed databases. All databases were potentially used for epidemiological studies. In addition, data on mortality, morbidity, disability, adverse events, quality of life, service/technology utilization, length of stay, and economics were also found in some databases. However, access to patient-level data was limited since information about the databases was not available on public sources.Our findings have shown that existing databases provided valuable information for HTA research with limitation on accessibility. Mutual dialogue on healthcare database development and usage for HTA among Asia-Pacific region is needed.

Healthcare Databases in Thailand and Japan: Potential Sources for Health Technology Assessment Research.

Science.gov (United States)

Saokaew, Surasak; Sugimoto, Takashi; Kamae, Isao; Pratoomsoot, Chayanin; Chaiyakunapruk, Nathorn

2015-01-01

Health technology assessment (HTA) has been continuously used for value-based healthcare decisions over the last decade. Healthcare databases represent an important source of information for HTA, which has seen a surge in use in Western countries. Although HTA agencies have been established in Asia-Pacific region, application and understanding of healthcare databases for HTA is rather limited. Thus, we reviewed existing databases to assess their potential for HTA in Thailand where HTA has been used officially and Japan where HTA is going to be officially introduced. Existing healthcare databases in Thailand and Japan were compiled and reviewed. Databases' characteristics e.g. name of database, host, scope/objective, time/sample size, design, data collection method, population/sample, and variables were described. Databases were assessed for its potential HTA use in terms of safety/efficacy/effectiveness, social/ethical, organization/professional, economic, and epidemiological domains. Request route for each database was also provided. Forty databases- 20 from Thailand and 20 from Japan-were included. These comprised of national censuses, surveys, registries, administrative data, and claimed databases. All databases were potentially used for epidemiological studies. In addition, data on mortality, morbidity, disability, adverse events, quality of life, service/technology utilization, length of stay, and economics were also found in some databases. However, access to patient-level data was limited since information about the databases was not available on public sources. Our findings have shown that existing databases provided valuable information for HTA research with limitation on accessibility. Mutual dialogue on healthcare database development and usage for HTA among Asia-Pacific region is needed.

Review and assessments of potential environmental, health and safety impacts of MHD technology. Final draft

Energy Technology Data Exchange (ETDEWEB)

1978-01-01

The purpose of this document is to develop an environmental, health and safety (EH and S) assessment and begin a site - specific assessment of these and socio - economic impacts for the magnetohydrodynamics program of the United States Department of Energy. This assessment includes detailed scientific and technical information on the specific EH and S issues mentioned in the MHD Environmental Development Plan. A review of current literature on impact-related subjects is also included. This document addresses the coal-fired, open-cycle MHD technology and reviews and assesses potential EH and S impacts resulting from operation of commercially-installed technology.

The Potential Relevance of Cognitive Neuroscience for the Development and Use of Technology-Enhanced Learning

Science.gov (United States)

Howard-Jones, Paul; Ott, Michela; van Leeuwen, Theo; De Smedt, Bert

2015-01-01

There is increasing interest in the application of cognitive neuroscience in educational thinking and practice, and here we review findings from neuroscience that demonstrate its potential relevance to technology-enhanced learning (TEL). First, we identify some of the issues in integrating neuroscientific concepts into TEL research. We caution…

The potential of crowdsourcing and mobile technology to support flood disaster risk reduction

Science.gov (United States)

See, Linda; McCallum, Ian; Liu, Wei; Mechler, Reinhard; Keating, Adriana; Hochrainer-Stigler, Stefan; Mochizuki, Junko; Fritz, Steffen; Dugar, Sumit; Arestegui, Michael; Szoenyi, Michael; Laso-Bayas, Juan-Carlos; Burek, Peter; French, Adam; Moorthy, Inian

2016-04-01

The last decade has seen a rise in citizen science and crowdsourcing for carrying out a variety of tasks across a number of different fields, most notably the collection of data such as the identification of species (e.g. eBird and iNaturalist) and the classification of images (e.g. Galaxy Zoo and Geo-Wiki). Combining human computing with the proliferation of mobile technology has resulted in vast amounts of geo-located data that have considerable value across multiple domains including flood disaster risk reduction. Crowdsourcing technologies, in the form of online mapping, are now being utilized to great effect in post-disaster mapping and relief efforts, e.g. the activities of Humanitarian OpenStreetMap, complementing official channels of relief (e.g. Haiti, Nepal and New York). Disaster event monitoring efforts have been further complemented with the use of social media (e.g. twitter for earthquakes, flood monitoring, and fire detection). Much of the activity in this area has focused on ex-post emergency management while there is considerable potential for utilizing crowdsourcing and mobile technology for vulnerability assessment, early warning and to bolster resilience to flood events. This paper examines the use of crowdsourcing and mobile technology for measuring and monitoring flood hazards, exposure to floods, and vulnerability, drawing upon examples from the literature and ongoing projects on flooding and food security at IIASA.

21st century natural product research and drug development and traditional medicines.

Science.gov (United States)

Ngo, Linh T; Okogun, Joseph I; Folk, William R

2013-04-01

Natural products and related structures are essential sources of new pharmaceuticals, because of the immense variety of functionally relevant secondary metabolites of microbial and plant species. Furthermore, the development of powerful analytical tools based upon genomics, proteomics, metabolomics, bioinformatics and other 21st century technologies are greatly expediting identification and characterization of these natural products. Here we discuss the synergistic and reciprocal benefits of linking these 'omics technologies with robust ethnobotanical and ethnomedical studies of traditional medicines, to provide critically needed improved medicines and treatments that are inexpensive, accessible, safe and reliable. However, careless application of modern technologies can challenge traditional knowledge and biodiversity that are the foundation of traditional medicines. To address such challenges while fulfilling the need for improved (and new) medicines, we encourage the development of Regional Centres of 'omics Technologies functionally linked with Regional Centres of Genetic Resources, especially in regions of the world where use of traditional medicines is prevalent and essential for health.

Bio-Intelligence: A Research Program Facilitating the Development of New Paradigms for Tomorrow's Patient Care

Science.gov (United States)

Phan, Sieu; Famili, Fazel; Liu, Ziying; Peña-Castillo, Lourdes

The advancement of omics technologies in concert with the enabling information technology development has accelerated biological research to a new realm in a blazing speed and sophistication. The limited single gene assay to the high throughput microarray assay and the laborious manual count of base-pairs to the robotic assisted machinery in genome sequencing are two examples to name. Yet even more sophisticated, the recent development in literature mining and artificial intelligence has allowed researchers to construct complex gene networks unraveling many formidable biological puzzles. To harness these emerging technologies to their full potential to medical applications, the Bio-intelligence program at the Institute for Information Technology, National Research Council Canada, aims to develop and exploit artificial intelligence and bioinformatics technologies to facilitate the development of intelligent decision support tools and systems to improve patient care - for early detection, accurate diagnosis/prognosis of disease, and better personalized therapeutic management.

Metabolomics through the lens of precision cardiovascular medicine.

Science.gov (United States)

Lam, Sin Man; Wang, Yuan; Li, Bowen; Du, Jie; Shui, Guanghou

2017-03-20

Metabolomics, which targets at the extensive characterization and quantitation of global metabolites from both endogenous and exogenous sources, has emerged as a novel technological avenue to advance the field of precision medicine principally driven by genomics-oriented approaches. In particular, metabolomics has revealed the cardinal roles that the environment exerts in driving the progression of major diseases threatening public health. Herein, the existent and potential applications of metabolomics in two key areas of precision cardiovascular medicine will be critically discussed: 1) the use of metabolomics in unveiling novel disease biomarkers and pathological pathways; 2) the contribution of metabolomics in cardiovascular drug development. Major issues concerning the statistical handling of big data generated by metabolomics, as well as its interpretation, will be briefly addressed. Finally, the need for integration of various omics branches and adopting a multi-omics approach to precision medicine will be discussed. Copyright © 2017 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

A potential disruptive technology in vaccine development: gene-based vaccines and their application to infectious diseases.

Science.gov (United States)

Kaslow, David C

2004-10-01

Vaccine development requires an amalgamation of disparate disciplines and has unique economic and regulatory drivers. Non-viral gene-based delivery systems, such as formulated plasmid DNA, are new and potentially disruptive technologies capable of providing 'cheaper, simpler, and more convenient-to-use' vaccines. Typically and somewhat ironically, disruptive technologies have poorer product performance, at least in the near-term, compared with the existing conventional technologies. Because successful product development requires that the product's performance must meet or exceed the efficacy threshold for a desired application, the appropriate selection of the initial product applications for a disruptive technology is critical for its successful evolution. In this regard, the near-term successes of gene-based vaccines will likely be for protection against bacterial toxins and acute viral and bacterial infections. Recent breakthroughs, however, herald increasing rather than languishing performance improvements in the efficacy of gene-based vaccines. Whether gene-based vaccines ultimately succeed in eliciting protective immunity in humans to persistent intracellular pathogens, such as HIV, malaria and tuberculosis, for which the conventional vaccine technologies have failed, remains to be determined. A success against any one of the persistent intracellular pathogens would be sufficient proof that gene-based vaccines represent a disruptive technology against which future vaccine technologies will be measured.

Recovery of valuable nitrogen compounds from agricultural liquid wastes: potential possibilities, bottlenecks and future technological challenges.

NARCIS (Netherlands)

Rulkens, W.H.; Klapwijk, A.; Willers, H.C.

1998-01-01

Agricultural liquid livestock wastes are an important potential source of valuable nitrogen-containing compounds such as ammonia and proteins. Large volumetric quantities of these wastes are produced in areas with a high livestock production density. Much technological research has been carried out

Potential applications of cryogenic technologies to plant genetic improvement and pathogen eradication.

Science.gov (United States)

Wang, Biao; Wang, Ren-Rui; Cui, Zhen-Hua; Bi, Wen-Lu; Li, Jing-Wei; Li, Bai-Quan; Ozudogru, Elif Aylin; Volk, Gayle M; Wang, Qiao-Chun

2014-01-01

Rapid increases in human populations provide a great challenge to ensure that adequate quantities of food are available. Sustainable development of agricultural production by breeding more productive cultivars and by increasing the productive potential of existing cultivars can help meet this demand. The present paper provides information on the potential uses of cryogenic techniques in ensuring food security, including: (1) long-term conservation of a diverse germplasm and successful establishment of cryo-banks; (2) maintenance of the regenerative ability of embryogenic tissues that are frequently the target for genetic transformation; (3) enhancement of genetic transformation and plant regeneration of transformed cells, and safe, long-term conservation for transgenic materials; (4) production and maintenance of viable protoplasts for transformation and somatic hybridization; and (5) efficient production of pathogen-free plants. These roles demonstrate that cryogenic technologies offer opportunities to ensure food security. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

The Potential of Digital Technologies for Transforming Informed Consent Practices with Children and Young People in Social Research

Directory of Open Access Journals (Sweden)

Sarah Parsons

2015-12-01

Full Text Available How children and young people understand and exercise their autonomy, engagement and decision-making is fundamental to learning how to become active and engaged citizens, and to be socially included. Digital technologies are increasingly an integral part of children’s everyday lives and, therefore, valuable tools for supporting social inclusion. This paper discusses how digital technologies might positively support autonomy, engagement and decision-making through the lens of informed consent practices within social research. Current research practices are dominated by paper-based methods for obtaining informed consent which could be exclusionary for children and young people generally, and children with additional learning and support needs in particular. Digital technologies (laptops, PCs, tablet devices, smartphones offer the potential to support accessibility and understanding of ideas and activities, as well as engagement with and autonomy in decision-making and participation. This paper explores this potential as well as the challenges that researchers may face in this context.

The Potential Use of Mobile Technology: Enhancing Accessibility and Communication in a Blended Learning Course

Science.gov (United States)

Mayisela, Tabisa

2013-01-01

Mobile technology is increasingly being used to support blended learning beyond computer centres. It has been considered as a potential solution to the problem of a shortage of computers for accessing online learning materials (courseware) in a blended learning course. The purpose of the study was to establish how the use of mobile technology…

Cutting through the Hype: Evaluating the Innovative Potential of New Educational Technologies through Business Model Analysis

Science.gov (United States)

Kalman, Yoram M.

2016-01-01

In an era when novel educational technologies are constantly introduced to the marketplace, often accompanied by hyperbolic claims that these ground-breaking innovations will transform the educational landscape, decision makers in educational institutions need a methodological approach for examining the innovative potential of new educational…

Exploring the Potential for Technology-Based Nutrition Education Among WIC Recipients in Remote Alaska Native Communities.

Science.gov (United States)

Power, Julianne M; Braun, Kathryn L; Bersamin, Andrea

Estimate media technology use in Alaska Native communities to inform the feasibility of technology-based nutrition education. A self-administered questionnaire was mailed to a random selection of about 50% of Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) authorized representatives in remote Alaska Native communities (n = 975). Media technology use, interest in media technology-based nutrition education, and potential barriers were assessed. Chi-square tests were used to investigate associations among technology use, age, and education. Technology use was common among respondents (n = 368); use was significantly more common among younger age groups and participants with a higher level of education. Smartphone (78.8%) and Facebook (95.8%) use was comparable to national averages, but having a computer at home (38.4%) was much less likely. Less than 50% of participants have Internet access at home. Findings shed light on new opportunities for WIC and other programs to deliver nutrition education to Alaska Native people in remote communities. Copyright © 2016 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

Sodium intake in US ethnic subgroups and potential impact of a new sodium reduction technology: NHANES Dietary Modeling.

Science.gov (United States)

Fulgoni, Victor L; Agarwal, Sanjiv; Spence, Lisa; Samuel, Priscilla

2014-12-18

Because excessive dietary sodium intake is a major contributor to hypertension, a reduction in dietary sodium has been recommended for the US population. Using the National Health and Nutrition Examination Survey (NHANES) 2007-2010 data, we estimated current sodium intake in US population ethnic subgroups and modeled the potential impact of a new sodium reduction technology on sodium intake. NHANES 2007-2010 data were analyzed using The National Cancer Institute method to estimate usual intake in population subgroups. Potential impact of SODA-LO® Salt Microspheres sodium reduction technology on sodium intake was modeled using suggested sodium reductions of 20-30% in 953 foods and assuming various market penetrations. SAS 9.2, SUDAAN 11, and NHANES survey weights were used in all calculations with assessment across age, gender and ethnic groups. Current sodium intake across all population subgroups exceeds the Dietary Guidelines 2010 recommendations and has not changed during the last decade. However, sodium intake measured as a function of food intake has decreased significantly during the last decade for all ethnicities. "Grain Products" and "Meat, Poultry, Fish, & Mixtures" contribute about 2/3rd of total sodium intake. Sodium reduction, using SODA-LO® Salt Microspheres sodium reduction technology (with 100% market penetration) was estimated to be 185-323 mg/day or 6.3-8.4% of intake depending upon age, gender and ethnic group. Current sodium intake in US ethnic subgroups exceeds the recommendations and sodium reduction technologies could potentially help reduce dietary sodium intake among those groups.

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.

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.

Nanotechnologies, technologies converging and potential biomedical applications

International Nuclear Information System (INIS)

Capuano, Vincenzo

2005-01-01

The applications of nanotechnology to biology and medicine appear really promising far diagnostics, for various therapeutic approaches and in medical instrumentations. The growing synergism among nanotechnology, biotechnology, information technology and cognitive sciences, their convergence (NBIC) from the nano scale, could involve on next decades great changes in medicine, from a reactive to a predictive and preventive approach. It is expected that NBIC converging technologies could achieve tremendous improvements in human abilities and enhance societal achievements. It appears therefore necessary a careful assessment of related social and ethical implications, in the framework of a constant dialogue between science and society [it

Aeroelastic Tailoring of Transport Aircraft Wings: State-of-the-Art and Potential Enabling Technologies

Science.gov (United States)

Jutte, Christine; Stanford, Bret K.

2014-01-01

This paper provides a brief overview of the state-of-the-art for aeroelastic tailoring of subsonic transport aircraft and offers additional resources on related research efforts. Emphasis is placed on aircraft having straight or aft swept wings. The literature covers computational synthesis tools developed for aeroelastic tailoring and numerous design studies focused on discovering new methods for passive aeroelastic control. Several new structural and material technologies are presented as potential enablers of aeroelastic tailoring, including selectively reinforced materials, functionally graded materials, fiber tow steered composite laminates, and various nonconventional structural designs. In addition, smart materials and structures whose properties or configurations change in response to external stimuli are presented as potential active approaches to aeroelastic tailoring.

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.

Report on the 10th anniversary of international drug discovery science and technology conference, 8 - 10 november 2012, nanjing, china.

Science.gov (United States)

Everett, Jeremy R

2013-03-01

The 10th Anniversary of International Drug Discovery Science and Technology (IDDST) Conference was held in Nanjing, China from 8 to 10 November 2012. The conference ran in parallel with the 2nd Annual Symposium of Drug Delivery Systems. Over 400 delegates from both conferences came together for the Opening Ceremony and Keynote Addresses but otherwise pursued separate paths in the huge facilities of the Nanjing International Expo Centre. The IDDST was arranged into 19 separate Chapters covering drug discovery biology, target validation, chemistry, rational drug design, pharmacology and toxicology, drug screening technology, 'omics' technologies, analytical, automation and enabling technologies, informatics, stem cells and regenerative medicine, bioprocessing, generics, biosimilars and biologicals and seven disease areas: cancer, CNS, respiratory and inflammation, autoimmune, emerging infectious, bone and orphan diseases. There were also two sessions of a 'Bench to Bedside to Business' Program and a Chinese Scientist programme. In each period of the IDDST conference, up to seven sessions were running in parallel. This Meeting Highlight samples just a fraction of the content of this large meeting. The talks included have as a link, the use of new approaches to drug discovery. Many other excellent talks could have been highlighted and the author has necessarily had to be selective.

Challenges of future aircraft propulsion: A review of distributed propulsion technology and its potential application for the all electric commercial aircraft

Science.gov (United States)

Gohardani, Amir S.; Doulgeris, Georgios; Singh, Riti

2011-07-01

This paper highlights the role of distributed propulsion technology for future commercial aircraft. After an initial historical perspective on the conceptual aspects of distributed propulsion technology and a glimpse at numerous aircraft that have taken distributed propulsion technology to flight, the focal point of the review is shifted towards a potential role this technology may entail for future commercial aircraft. Technological limitations and challenges of this specific technology are also considered in combination with an all electric aircraft concept, as means of predicting the challenges associated with the design process of a next generation commercial aircraft.

Towards the Biological Understanding of CTC: Capture Technologies, Definitions and Potential to Create Metastasis

Directory of Open Access Journals (Sweden)

Ana M.C. Barradas

2013-12-01

Full Text Available Circulating Tumor Cells (CTC are rare cells originated from tumors that travel into the blood stream, extravasate to different organs of which only a small fraction will develop into metastasis. The presence of CTC enumerated with the CellSearch system is associated with a relative short survival and their continued presence after the first cycles of therapy indicates a futile therapy in patients with metastatic carcinomas. Detailed characterization of CTC holds the promise to enable the choice of the optimal therapy for the individual patients during the course of the disease. The phenotype, physical and biological properties are however not well understood making it difficult to assess the merit of recent technological advancements to improve upon the capture of CTC or to evaluate their metastatic potential. Here we will discuss the recent advances in the classification of CTC captured by the CellSearch system, the implications of their features and numbers. Latest capture platforms are reviewed and placed in the light of technology improvements needed to detect CTC. Physical properties, phenotype, viability and proliferative potential and means to assess their proliferation and metastatic capacity will be summarized and placed in the context of the latest CTC capture platforms.

"It's all about incentive": Social technology as a potential facilitator for self-determined physical activity participation for young people with physical disabilities.

Science.gov (United States)

Knibbe, Tara Joy; McPherson, Amy C; Gladstone, Brenda; Biddiss, Elaine

2017-09-29

To investigate the perceived role of social technologies in promoting physical activity participation for young people with physical disabilities and to identify design considerations that should be addressed when creating social technologies to promote physical activity. Interactive design workshops for young people with physical disabilities aged 12-18 (n = 8) were held. Data were analyzed using interpretive thematic analysis. Young people perceived significant benefit for social technologies to promote physical activity as they have the potential to overcome many barriers to physical activity participation. Design features recommended by the participants included (1) options for diverse interests and preferences, (2) provision of informational support, (3) support through equitable technology design, (4) incentive through competition and play, and (5) opportunities to develop community. Social technology has potential to provide tailored, equitable opportunities for social engagement and physical activity participation for young people with physical disabilities through needs- and preference-specific design.

Discussion on the application potential of thermal infrared remote sensing technology in uranium deposits exploration

International Nuclear Information System (INIS)

Wang Junhu; Zhang Jielin; Liu Dechang

2011-01-01

With the continual development of new thermal infrared sensors and thermal radiation theory, the technology of thermal infrared remote sensing has shown great potential for applications in resources exploration, especially in the field of uranium exploration. The paper makes a systemic summary of the theoretical basis and research status of the thermal infrared remote sensing applications in resources exploration from the surface temperature, thermal inertia and thermal infrared spectrum. What's more, the research objective and the research content of thermal infrared remote sensing in the uranium deposits exploration applications are discussed in detail. Besides, based on the thermal infrared ASTER data, the paper applies this technology to the granite-type uranium deposits in South China and achieves good result. Above all, the practice proves that the thermal infrared remote sensing technology has a good application prospects and particular value in the field of uranium prospecting and will play an important role in the prospecting target of the uranium deposits. (authors)

Investigation of greenhouse gas reduction potential and change in technological selection in Indian power sector

International Nuclear Information System (INIS)

Mathur, Jyotirmay; Bansal, Narendra Kumar; Wagner, H.-J.

2003-01-01

Due to the growing energy needs along with increasing concerns towards control of greenhouse gas emissions, most developing countries are under pressure to find alternative methods for energy conversion and policies to make these technologies economically viable. One of the instruments that have been adopted by many industrial countries is that of the carbon tax. The rate of introducing carbon taxes however, depends upon the local economic conditions and market forces. The case of Indian power sector has been examined by using MARKAL model for introduction of carbon taxes at four different trajectories. Their implications on the power generation choices have been investigated for a time span of 25 years from the year 2000. In general large hydropower plants have emerged as the first choice followed by wind energy systems. However, cheaper availability of coal in India keeps scope of use of coal based technologies for which pressurised fluidised bed combustion technology has been found to be the balanced choice among fossil technologies. There exists a potential of reduction of greenhouse gas emissions by about 25% as compared to the 'business-as-usual' case in presence of high carbon tax rates

Complexity and conundrums. Citizens' evaluations of potentially contentious novel food technologies using a deliberative discourse approach.

Science.gov (United States)

Greehy, Gráinne M; McCarthy, Mary B; Henchion, Maeve M; Dillon, Emma J; McCarthy, Sinéad N

2013-11-01

This research considers the processes involved in the formation of attitudes by citizens on potentially contentious novel food technologies (NFTs). Observations of one-to-one deliberative discourses between food scientists and citizens, during which they discussed these technologies, form the basis of this enquiry. This approach enables an exploration of how individuals construct meaning around as well as interpret information about the technologies. Thematic analysis identifies key features that provide the frameworks for citizens' evaluations. How individuals make sense of these technologies is shaped by their beliefs, values and personal characteristics; their perceptions of power and control over the development and sale of NFT related products; and, the extent to which these products are relevant to their personal lives. Internal negotiations between these influences are evident, and evaluations are based on the relative importance of each influence to the individual. Internal conflicts and tensions are associated with citizens' evolving evaluative processes, which may in turn present as attitude ambivalence and instability. Many challenges are linked with engaging with the general public about these technologies, as levels of knowledge, understanding and interest vary. Copyright © 2013 Elsevier Ltd. All rights reserved.

Development and potential applications of CRISPR-Cas9 genome editing technology in sarcoma.

Science.gov (United States)

Liu, Tang; Shen, Jacson K; Li, Zhihong; Choy, Edwin; Hornicek, Francis J; Duan, Zhenfeng

2016-04-01

Sarcomas include some of the most aggressive tumors and typically respond poorly to chemotherapy. In recent years, specific gene fusion/mutations and gene over-expression/activation have been shown to drive sarcoma pathogenesis and development. These emerging genomic alterations may provide targets for novel therapeutic strategies and have the potential to transform sarcoma patient care. The RNA-guided nuclease CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein-9 nuclease) is a convenient and versatile platform for site-specific genome editing and epigenome targeted modulation. Given that sarcoma is believed to develop as a result of genetic alterations in mesenchymal progenitor/stem cells, CRISPR-Cas9 genome editing technologies hold extensive application potentials in sarcoma models and therapies. We review the development and mechanisms of the CRISPR-Cas9 system in genome editing and introduce its application in sarcoma research and potential therapy in clinic. Additionally, we propose future directions and discuss the challenges faced with these applications, providing concise and enlightening information for readers interested in this area. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The potential of quantum technology gravity sensors in civil engineering

Science.gov (United States)

Tuckwell, G.; Metje, N.; Boddice, D.; Usher, C.

2017-12-01

Potential field techniques have advantages over active geophysical techniques as they are not limited to the depth they can image features, provided the signals of interest are detectable amongst the other variations recorded by the instrument. A new generation of gravity instruments based on quantum technology promise greatly increased measurement sensitivity, but with this comes significant challenges in data processing and noise suppression. In the UK Innovate UK funded SIGMA project (http://www.rsksigma.co.uk/) the field of opportunity for a step change in gravity sensor accuracy has been evaluated by comparison with existing geophysical sensors, identifying the range of targets and depths of interest to commercial end users that are currently undetectable and might become visible. Forward modelling was used to quantify the potential of a Quantum Technology (QT) gravity and gravity gradiometer sensor. A substantive improvement in detectability of targets is predicted, which can be considered as a factor of 1.5 to 2 increase in the depth of detectability, or in the reduction of the size of the feature of interest. To take further advantage of new instrument sensitivity, new survey workflows are required. The accuracy of measured gravity maps is limited by environmental vibration noise, and by the accuracy with which tidal variations and terrain signals can be removed. It is still common practice in engineering scale surveys for gravity values to be reduced to Bouguer residuals. However, with a more sensitive instrument comes the need to measure the terrain more accurately. This can be achieved within a commercially viable workflow using a laser scanner for rapid data acquisition and advanced processing to produce an accurate DEM. Initial tests on 4 commercial sites have shown that an improvement of 10s of mGal can be achieved if applying a full digital terrain model correction to the microgravity data even on sites with very minor topographic height variations

Precision medicine for psychopharmacology: a general introduction.

Science.gov (United States)

Shin, Cheolmin; Han, Changsu; Pae, Chi-Un; Patkar, Ashwin A

2016-07-01

Precision medicine is an emerging medical model that can provide accurate diagnoses and tailored therapeutic strategies for patients based on data pertaining to genes, microbiomes, environment, family history and lifestyle. Here, we provide basic information about precision medicine and newly introduced concepts, such as the precision medicine ecosystem and big data processing, and omics technologies including pharmacogenomics, pharamacometabolomics, pharmacoproteomics, pharmacoepigenomics, connectomics and exposomics. The authors review the current state of omics in psychiatry and the future direction of psychopharmacology as it moves towards precision medicine. Expert commentary: Advances in precision medicine have been facilitated by achievements in multiple fields, including large-scale biological databases, powerful methods for characterizing patients (such as genomics, proteomics, metabolomics, diverse cellular assays, and even social networks and mobile health technologies), and computer-based tools for analyzing large amounts of data.

Systematic approach to understanding the pathogenesis of systemic sclerosis.

Science.gov (United States)

Zuo, Xiaoxia; Zhang, Lihua; Luo, Hui; Li, Yisha; Zhu, Honglin

2017-10-01

Systemic sclerosis (SSc) is a complex heterogeneous autoimmune disease. Progressive organ fibrosis is a major contributor to SSc mortality. Despite extensive efforts, the underlying mechanism of SSc remains unclear. Efforts to understand the pathogenesis of SSc have included genomics, epigenetics, transcriptomic, proteomic and metabolomic studies in the last decade. This review focuses on recent studies in SSc research based on multi-omics. The combination of these technologies can help us understand the pathogenesis of SSc. This review aims to provide important information for disease identification, therapeutic targets and potential biomarkers. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Respiratory Pathways Reconstructed by Multi-Omics Analysis in Melioribacter roseus, Residing in a Deep Thermal Aquifer of the West-Siberian Megabasin

Science.gov (United States)

Gavrilov, Sergey; Podosokorskaya, Olga; Alexeev, Dmitry; Merkel, Alexander; Khomyakova, Maria; Muntyan, Maria; Altukhov, Ilya; Butenko, Ivan; Bonch-Osmolovskaya, Elizaveta; Govorun, Vadim; Kublanov, Ilya

2017-01-01

Melioribacter roseus, a representative of recently proposed Ignavibacteriae phylum, is a metabolically versatile thermophilic bacterium, inhabiting subsurface biosphere of the West-Siberian megabasin and capable of growing on various substrates and electron acceptors. Genomic analysis followed by inhibitor studies and membrane potential measurements of aerobically grown M. roseus cells revealed the activity of aerobic respiratory electron transfer chain comprised of respiratory complexes I and IV, and an alternative complex III. Phylogeny reconstruction revealed that oxygen reductases belonged to atypical cc(o/b)o3-type and canonical cbb3–type cytochrome oxidases. Also, two molybdoenzymes of M. roseus were affiliated either with Ttr or Psr/Phs clades, but not with typical respiratory arsenate reductases of the Arr clade. Expression profiling, both at transcripts and protein level, allowed us to assign the role of the terminal respiratory oxidase under atmospheric oxygen concentration for the cc(o/b)o3 cytochrome oxidase, previously proposed to serve for oxygen detoxification only. Transcriptomic analysis revealed the involvement of both molybdoenzymes of M. roseus in As(V) respiration, yet differences in the genomic context of their gene clusters allow to hypothesize about their distinct roles in arsenate metabolism with the ‘Psr/Phs’-type molybdoenzyme being the most probable candidate respiratory arsenate reductase. Basing on multi-omics data, the pathways for aerobic and arsenate respiration were proposed. Our results start to bridge the vigorously increasing gap between homology-based predictions and experimentally verified metabolic processes, what is especially important for understudied microorganisms of novel lineages from deep subsurface environments of Eurasia, which remained separated from the rest of the biosphere for several geological periods. PMID:28713355

Respiratory Pathways Reconstructed by Multi-Omics Analysis in Melioribacter roseus, Residing in a Deep Thermal Aquifer of the West-Siberian Megabasin

Directory of Open Access Journals (Sweden)

Sergey Gavrilov

2017-06-01

Full Text Available Melioribacter roseus, a representative of recently proposed Ignavibacteriae phylum, is a metabolically versatile thermophilic bacterium, inhabiting subsurface biosphere of the West-Siberian megabasin and capable of growing on various substrates and electron acceptors. Genomic analysis followed by inhibitor studies and membrane potential measurements of aerobically grown M. roseus cells revealed the activity of aerobic respiratory electron transfer chain comprised of respiratory complexes I and IV, and an alternative complex III. Phylogeny reconstruction revealed that oxygen reductases belonged to atypical cc(o/bo3-type and canonical cbb3–type cytochrome oxidases. Also, two molybdoenzymes of M. roseus were affiliated either with Ttr or Psr/Phs clades, but not with typical respiratory arsenate reductases of the Arr clade. Expression profiling, both at transcripts and protein level, allowed us to assign the role of the terminal respiratory oxidase under atmospheric oxygen concentration for the cc(o/bo3 cytochrome oxidase, previously proposed to serve for oxygen detoxification only. Transcriptomic analysis revealed the involvement of both molybdoenzymes of M. roseus in As(V respiration, yet differences in the genomic context of their gene clusters allow to hypothesize about their distinct roles in arsenate metabolism with the ‘Psr/Phs’-type molybdoenzyme being the most probable candidate respiratory arsenate reductase. Basing on multi-omics data, the pathways for aerobic and arsenate respiration were proposed. Our results start to bridge the vigorously increasing gap between homology-based predictions and experimentally verified metabolic processes, what is especially important for understudied microorganisms of novel lineages from deep subsurface environments of Eurasia, which remained separated from the rest of the biosphere for several geological periods.

EU Framework 6 Project: Predictive Toxicology (PredTox)-overview and outcome

International Nuclear Information System (INIS)

Suter, Laura; Schroeder, Susanne; Meyer, Kirstin; Gautier, Jean-Charles; Amberg, Alexander; Wendt, Maria; Gmuender, Hans; Mally, Angela; Boitier, Eric; Ellinger-Ziegelbauer, Heidrun; Matheis, Katja; Pfannkuch, Friedlieb

2011-01-01

In this publication, we report the outcome of the integrated EU Framework 6 Project: Predictive Toxicology (PredTox), including methodological aspects and overall conclusions. Specific details including data analysis and interpretation are reported in separate articles in this issue. The project, partly funded by the EU, was carried out by a consortium of 15 pharmaceutical companies, 2 SMEs, and 3 universities. The effects of 16 test compounds were characterized using conventional toxicological parameters and 'omics' technologies. The three major observed toxicities, liver hypertrophy, bile duct necrosis and/or cholestasis, and kidney proximal tubular damage were analyzed in detail. The combined approach of 'omics' and conventional toxicology proved a useful tool for mechanistic investigations and the identification of putative biomarkers. In our hands and in combination with histopathological assessment, target organ transcriptomics was the most prolific approach for the generation of mechanistic hypotheses. Proteomics approaches were relatively time-consuming and required careful standardization. NMR-based metabolomics detected metabolite changes accompanying histopathological findings, providing limited additional mechanistic information. Conversely, targeted metabolite profiling with LC/GC-MS was very useful for the investigation of bile duct necrosis/cholestasis. In general, both proteomics and metabolomics were supportive of other findings. Thus, the outcome of this program indicates that 'omics' technologies can help toxicologists to make better informed decisions during exploratory toxicological studies. The data support that hypothesis on mode of action and discovery of putative biomarkers are tangible outcomes of integrated 'omics' analysis. Qualification of biomarkers remains challenging, in particular in terms of identification, mechanistic anchoring, appropriate specificity, and sensitivity.

Solar photovoltaic markets, economics, technology, and potential

Energy Technology Data Exchange (ETDEWEB)

Blais, J.M.J.; Molinski, T.S. [Manitoba Hydro, Winnipeg, MB (Canada)]|[Emerging Energy Systems, Islamabad (Pakistan)

2008-07-01

Solar Photovoltaics (PV) are solid state semiconductor electronic devices that transform infrared, visible, or ultraviolet light energy from the sun directly into electrical energy. Selenium was used to create the first solar cell in 1883. In 1954, Bell Laboratories developed the modern day silicon solar cell, whereby impurities were added to silicon through a process called doping. Silicon doped with boron results in a positive electrical charge, while silicon doped with phosphorous results in a negative electrical charge. The atom collision from photons in sunlight provides the necessary energy to free a trapped electron in the doped silicon, which then may flow through a wire creating an electric current. Many different materials besides silicon are used to create solar cells, such as plastics, organic compounds, and theoretically even special paints, while other doping agents besides boron and phosphorous are also used, such as arsenic and gallium. This paper provided an introduction to solar PV and world solar PV growth and markets. A review of solar PV economics was also included. In 2008, the total installed costs of solar photovoltaic cells were in the range of 7 to 10 Canadian dollars. In addition, the advantages and disadvantages of solar PV were presented. Solar technologies under research and development were also discussed and assessed. It was concluded that although solar PV was one of the most expensive forms of renewable generation, there is great potential for solar PV to gain broader based application as costs continue to drop. 11 refs., 1 tab., 1 fig.

Exploring the potential impact of implementing carbon capture technologies in fossil fuel power plants on regional European water stress index levels

NARCIS (Netherlands)

Schakel, W.B.; Pfister, Stephan; Ramirez, C.A.