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Sample records for scientists map epigenome

  1. CpG island mapping by epigenome prediction.

    Directory of Open Access Journals (Sweden)

    Christoph Bock

    2007-06-01

    Full Text Available CpG islands were originally identified by epigenetic and functional properties, namely, absence of DNA methylation and frequent promoter association. However, this concept was quickly replaced by simple DNA sequence criteria, which allowed for genome-wide annotation of CpG islands in the absence of large-scale epigenetic datasets. Although widely used, the current CpG island criteria incur significant disadvantages: (1 reliance on arbitrary threshold parameters that bear little biological justification, (2 failure to account for widespread heterogeneity among CpG islands, and (3 apparent lack of specificity when applied to the human genome. This study is driven by the idea that a quantitative score of "CpG island strength" that incorporates epigenetic and functional aspects can help resolve these issues. We construct an epigenome prediction pipeline that links the DNA sequence of CpG islands to their epigenetic states, including DNA methylation, histone modifications, and chromatin accessibility. By training support vector machines on epigenetic data for CpG islands on human Chromosomes 21 and 22, we identify informative DNA attributes that correlate with open versus compact chromatin structures. These DNA attributes are used to predict the epigenetic states of all CpG islands genome-wide. Combining predictions for multiple epigenetic features, we estimate the inherent CpG island strength for each CpG island in the human genome, i.e., its inherent tendency to exhibit an open and transcriptionally competent chromatin structure. We extensively validate our results on independent datasets, showing that the CpG island strength predictions are applicable and informative across different tissues and cell types, and we derive improved maps of predicted "bona fide" CpG islands. The mapping of CpG islands by epigenome prediction is conceptually superior to identifying CpG islands by widely used sequence criteria since it links CpG island detection to

  2. A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells

    Science.gov (United States)

    This report presents a study utilizing next-generation sequencing technology, combined with chromatin immunoprecipitation (ChIP-seq) technology to analyze histone modification induced by butyrate and to construct a high-definition map of the epigenomic landscape with normal histone H3, H4, and their...

  3. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

    DEFF Research Database (Denmark)

    Xiang, Hui; Zhu, Jingde; Chen, Quan

    2010-01-01

    Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic...... and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis and human, demonstrates...... a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation....

  4. Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map.

    Science.gov (United States)

    Hardcastle, Thomas J; Müller, Sebastian Y; Baulcombe, David C

    2018-04-20

    Based on 98 public and internal small RNA high throughput sequencing libraries, we mapped small RNAs to the genome of the model organism Arabidopsis thaliana and defined loci based on their expression using an empirical Bayesian approach. The resulting loci were subsequently classified based on their genetic and epigenetic context as well as their expression properties. We present the results of this classification, which broadly conforms to previously reported divisions between transcriptional and post-transcriptional gene silencing small RNAs, and to PolIV and PolV dependencies. However, we are able to demonstrate the existence of further subdivisions in the small RNA population of functional significance. Moreover, we present a framework for similar analyses of small RNA populations in all species.

  5. High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure.

    Science.gov (United States)

    Rosa-Garrido, Manuel; Chapski, Douglas J; Schmitt, Anthony D; Kimball, Todd H; Karbassi, Elaheh; Monte, Emma; Balderas, Enrique; Pellegrini, Matteo; Shih, Tsai-Ting; Soehalim, Elizabeth; Liem, David; Ping, Peipei; Galjart, Niels J; Ren, Shuxun; Wang, Yibin; Ren, Bing; Vondriska, Thomas M

    2017-10-24

    Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined. To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype. Transcriptome analyses by RNA-seq were conducted as a functional readout of the epigenomic structural changes. Depletion of CTCF was sufficient to induce heart failure in mice, and human patients with heart failure receiving mechanical unloading via left ventricular assist devices show increased CTCF abundance. Chromatin structural analyses revealed interactions within the cardiac myocyte genome at 5-kb resolution, enabling examination of intra- and interchromosomal events, and providing a resource for future cardiac epigenomic investigations. Pressure overload or CTCF depletion selectively altered boundary strength between topologically associating domains and A/B compartmentalization, measurements of genome accessibility. Heart failure involved decreased stability of chromatin interactions around disease-causing genes. In addition, pressure overload or CTCF depletion remodeled long-range interactions of cardiac enhancers, resulting in a significant decrease in local chromatin interactions around these functional elements. These findings provide a high-resolution chromatin architecture resource for cardiac epigenomic investigations and demonstrate that global structural remodeling of chromatin underpins heart failure. The newly identified principles of endogenous chromatin structure have key implications for epigenetic therapy. © 2017 The Authors.

  6. Perspectives of International Human Epigenome Consortium

    Directory of Open Access Journals (Sweden)

    Jae-Bum Bae

    2013-03-01

    Full Text Available As the International Human Epigenome Consortium (IHEC launched officially at the 2010 Washington meeting, a giant step toward the conquest of unexplored regions of the human genome has begun. IHEC aims at the production of 1,000 reference epigenomes to the international scientific community for next 7-10 years. Seven member institutions, including South Korea, Korea National Institute of Health (KNIH, will produce 25-200 reference epigenomes individually, and the produced data will be publically available by using a data center. Epigenome data will cover from whole genome bisulfite sequencing, histone modification, and chromatin access information to miRNA-seq. The final goal of IHEC is the production of reference maps of human epigenomes for key cellular status relevant to health and disease.

  7. Genome-wide ChIP-seq mapping and analysis of butyrate-induced H3K9 and H3K27 acetylation and epigenomic landscape alteration in bovine cells

    Science.gov (United States)

    Utilizing next-generation sequencing technology, combined with ChIP (Chromatin Immunoprecipitation) technology, we analyzed histone modification (acetylation) induced by butyrate and the large-scale mapping of the epigenomic landscape of normal histone H3 and acetylated histone H3K9 and H3K27. To d...

  8. What Is the Epigenome?

    Science.gov (United States)

    ... research is being done with the Human Epigenome Project . The University of Utah provides an interactive epigenetics tutorial . The National Human Genome Research Institute provides a fact sheet on Epigenomics. ...

  9. Study on radiation-responsive epigenomes

    International Nuclear Information System (INIS)

    Kim, Jin Hong; Lee, Seung Sik; Bae, Hyung Woo; Kim, Ji Hong; Kim, Ji Eun; Cho, Eun Ju; Lee, Min Hee; Moon, Yu Ran

    2012-01-01

    The purpose of this project is development of world-class headspring techniques of biological science for application of plant genomes/epigenomes through study on radiation- responsive epigenomes and improvement of the national competitiveness in the field of fundamental technology for biological science and industry. Research scope includes 1) Investigation of radiation-responsive epigenomes and elucidation of their relation with phenotypes, 2) Elucidation of interaction and transcription control of epigenomes and epigenetic regulators using IR, 3) Investigation of epigenome-mediated traits in plant development, differentiation and antioxidant defense using IR, and 4) Development of application techniques of radiation-responsive epigenomes for eco-monitoring and molecular breeding. Main results are as follow: practical application of ChIP in GR-treated Arabidopsis using anti-histone antibodies: mapping of DNA methylomes associated with GR-responsive transcriptomes: setup of methylated DNA quantification using HPLC: elucidation of aberrations in epigenetic regulation induced by low-dose GR using gamma phytotron: comparison of gene expression of histone-modifying enzymes after treatment of GR: elucidation of transcriptomes and physiological alterations associated with delayed senescence of drd1-6 mutant: comparison of gene expression of DNA methylation-related enzymes in GR-treated rice callus and Arabidopsis: investigation of germination capacity, low-temperature, salinity and drought stress-resistance in drd1-6 epigenetic mutant: investigation of aberrations in DNA methylation depending on dose rates of gamma radiation

  10. NIH Scientists Map Genetic Changes That Drive Tumors in a Common Pediatric Soft-Tissue Cancer

    Science.gov (United States)

    ... Press Release NIH scientists map genetic changes that drive tumors in a common pediatric soft-tissue cancer ... of Health FOLLOW US Facebook Twitter Instagram YouTube Google+ LinkedIn GovDelivery RSS CONTACT INFORMATION Contact Us LiveHelp ...

  11. Epigenomic programing: a future way to health?

    Directory of Open Access Journals (Sweden)

    Boris A. Shenderov

    2014-05-01

    Full Text Available It is now generally accepted that the ‘central genome dogma’ (i.e. a causal chain going from DNA to RNA to proteins and downstream to biological functions should be replaced by the ‘fluid genome dogma’, that is, complex feed-forward and feed-back cycles that interconnect organism and environment by epigenomic programing – and reprograming – throughout life and at all levels, sometimes also down the generations. The epigenomic programing is the net sum of interactions derived from own metabolism and microbiota as well as external factors such as diet, pharmaceuticals, environmental compounds, and so on. It is a growing body of results indicating that many chronic metabolic and degenerative disorders and diseases – often called ‘civilization diseases’ – are initiated and/or influenced upon by non-optimal epigenomic programing, often taking place early in life. In this context, the first 1,000 days of life – from conception into early infancy – is often called the most important period of life. The following sections present some major mechanisms for epigenomic programing as well as some factors assumed to be of importance. The need for more information about own genome and metagenome, as well as a substantial lack of adequate information regarding dietary and environmental databases are also commented upon. However, the mere fact that we can influence epigenomic health programing opens up the way for prophylactic and therapeutic interventions. The authors underline the importance of creating a ‘Human Gut Microbiota and Epigenomic Platform’ in order to facilitate interdisciplinary collaborations among scientists and clinicians engaged in host microbial ecology, nutrition, metagenomics, epigenomics and metabolomics as well as in disease epidemiology, prevention and treatment.

  12. Time for the epigenome

    CERN Multimedia

    2010-01-01

    The complexity of genetic regulation is one of the great wonders of nature, but it represents a daunting challenge to unravel. The International Human Epigenome Consortium is an appropriate response. ( 1 page)

  13. Using Author Bylines and Concept Maps to Illustrate the Connectedness of Scientists

    Directory of Open Access Journals (Sweden)

    Min-Ken Liao

    2013-02-01

    Full Text Available Incorporating reading and discussing primary articles in undergraduate courses has been shown to enhance students’ learning, stimulate their interests in science, and retain them as science majors.  While instructors diligently coach students to scrutinize every section in an article thoroughly and critically, the author byline is often overlooked.  In this study, the author bylines of primary articles were used to illustrate the connectedness of scientists and the collaborative nature of science.  First year college students first learned how to construct a concept map and used concept maps to connect 14 scientists with 14 primary articles that these scientists authored.  In doing so, students visualized and understood science as human activity and science progresses as a community effort.  Pre- and post-activity questionnaires were used to evaluate whether the activity objectives were met.  Students further examined the structure and organization of a primary article after the activity and they were engaged in discussions such as how research ideas developed and evolved, the advantages and disadvantages of collaborative research, the ethics of authorships, graduate schools, and careers in science. Hopefully, perceiving the authors of primary articles as real people in a social network and science as the collaborative efforts may help students see themselves being a part of the scientific advancement and inspire them to pursue careers in science.

  14. Epigenomics of hypertension.

    Science.gov (United States)

    Liang, Mingyu; Cowley, Allen W; Mattson, David L; Kotchen, Theodore A; Liu, Yong

    2013-07-01

    Multiple genes and pathways are involved in the pathogenesis of hypertension. Epigenomic studies of hypertension are beginning to emerge and hold great promise of providing novel insights into the mechanisms underlying hypertension. Epigenetic marks or mediators including DNA methylation, histone modifications, and noncoding RNA can be studied at a genome or near-genome scale using epigenomic approaches. At the single gene level, several studies have identified changes in epigenetic modifications in genes expressed in the kidney that correlate with the development of hypertension. Systematic analysis and integration of epigenetic marks at the genome-wide scale, demonstration of cellular and physiological roles of specific epigenetic modifications, and investigation of inheritance are among the major challenges and opportunities for future epigenomic and epigenetic studies of hypertension. © 2013 Elsevier Inc. All rights reserved.

  15. Epigenomics in marine fishes.

    Science.gov (United States)

    Metzger, David C H; Schulte, Patricia M

    2016-12-01

    Epigenetic mechanisms are an underappreciated and often ignored component of an organism's response to environmental change and may underlie many types of phenotypic plasticity. Recent technological advances in methods for detecting epigenetic marks at a whole-genome scale have launched new opportunities for studying epigenomics in ecologically relevant non-model systems. The study of ecological epigenomics holds great promise to better understand the linkages between genotype, phenotype, and the environment and to explore mechanisms of phenotypic plasticity. The many attributes of marine fish species, including their high diversity, variable life histories, high fecundity, impressive plasticity, and economic value provide unique opportunities for studying epigenetic mechanisms in an environmental context. To provide a primer on epigenomic research for fish biologists, we start by describing fundamental aspects of epigenetics, focusing on the most widely studied and most well understood of the epigenetic marks: DNA methylation. We then describe the techniques that have been used to investigate DNA methylation in marine fishes to date and highlight some new techniques that hold great promise for future studies. Epigenomic research in marine fishes is in its early stages, so we first briefly discuss what has been learned about the establishment, maintenance, and function of DNA methylation in fishes from studies in zebrafish and then summarize the studies demonstrating the pervasive effects of the environment on the epigenomes of marine fishes. We conclude by highlighting the potential for ongoing research on the epigenomics of marine fishes to reveal critical aspects of the interaction between organisms and their environments. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Designing a Sustainable Noise Mapping System Based on Citizen Scientists Smartphone Sensor Data.

    Directory of Open Access Journals (Sweden)

    Eunyoung Shim

    Full Text Available In this study, we attempted to assess the feasibility of collecting population health data via mobile devices. Specifically, we constructed noise maps based on sound information monitored by individuals' smartphones. We designed a sustainable way of creating noise maps that can overcome the shortcomings of existing station-based noise-monitoring systems. Three hundred and nine Seoul residents aged 20-49 years who used Android-based smartphones were recruited, and the subjects installed a special application that we developed for this study. This application collected information on sound and geographical location every 10 min for 7 days. Using GIS, we were able to construct various types of noise maps of Seoul (e.g., daytime/nighttime and weekdays/weekends using the information on sound and geographical location obtained via the users' smartphones. Despite the public health importance of noise management, a number of countries and cities lack a sustainable system to monitor noise. This pilot study showed the possibility of using the smartphones of citizen scientists as an economical and sustainable way of monitoring noise, particularly in an urban context in developing countries.

  17. Designing a Sustainable Noise Mapping System Based on Citizen Scientists Smartphone Sensor Data.

    Science.gov (United States)

    Shim, Eunyoung; Kim, Dohyeong; Woo, Hyekyung; Cho, Youngtae

    2016-01-01

    In this study, we attempted to assess the feasibility of collecting population health data via mobile devices. Specifically, we constructed noise maps based on sound information monitored by individuals' smartphones. We designed a sustainable way of creating noise maps that can overcome the shortcomings of existing station-based noise-monitoring systems. Three hundred and nine Seoul residents aged 20-49 years who used Android-based smartphones were recruited, and the subjects installed a special application that we developed for this study. This application collected information on sound and geographical location every 10 min for 7 days. Using GIS, we were able to construct various types of noise maps of Seoul (e.g., daytime/nighttime and weekdays/weekends) using the information on sound and geographical location obtained via the users' smartphones. Despite the public health importance of noise management, a number of countries and cities lack a sustainable system to monitor noise. This pilot study showed the possibility of using the smartphones of citizen scientists as an economical and sustainable way of monitoring noise, particularly in an urban context in developing countries.

  18. The Aging Epigenome

    Science.gov (United States)

    Booth, Lauren N.

    2016-01-01

    During aging, the mechanisms that normally maintain health and stress resistance strikingly decline, resulting in decrepitude, frailty, and ultimately death. Exactly when and how this decline occurs is unknown. Changes in transcriptional networks and chromatin state lie at the heart of age-dependent decline. These epigenomic changes are not only observed during aging but also profoundly affect cellular function and stress resistance, thereby contributing to the progression of aging. We propose that the dysregulation of transcriptional and chromatin networks is a crucial component of aging. Understanding age-dependent epigenomic changes will yield key insights into how aging begins and progresses and should lead to the development of new therapeutics that delay or even reverse aging and age-related diseases. PMID:27259204

  19. Epigenomics of Sarcomas

    OpenAIRE

    Guilhamon, P. C. M.

    2014-01-01

    Isocitrate dehydrogenase (IDH) genes 1 and 2 are frequently mutated in acute myeloid leukemia (AML), lower-grade glioma (LGG), and cholangiocarcinoma (CC). In these three malignancies, mutant IDH status is associated with increased 2-hydroxyglutarate (2-HG) production and a DNA hypermethylation phenotype, implicating altered epigenome dynamics in the aetiology of these cancers. Here I show that the IDH variants in chondrosarcoma (CS) are also associated with a hypermethylation phenotype, supp...

  20. Epigenomics in cancer management

    International Nuclear Information System (INIS)

    Costa, Fabricio F

    2010-01-01

    The identification of all epigenetic modifications implicated in gene expression is the next step for a better understanding of human biology in both normal and pathological states. This field is referred to as epigenomics, and it is defined as epigenetic changes (ie, DNA methylation, histone modifications and regulation by noncoding RNAs such as microRNAs) on a genomic scale rather than a single gene. Epigenetics modulate the structure of the chromatin, thereby affecting the transcription of genes in the genome. Different studies have already identified changes in epigenetic modifications in a few genes in specific pathways in cancers. Based on these epigenetic changes, drugs against different types of tumors were developed, which mainly target epimutations in the genome. Examples include DNA methylation inhibitors, histone modification inhibitors, and small molecules that target chromatin-remodeling proteins. However, these drugs are not specific, and side effects are a major problem; therefore, new DNA sequencing technologies combined with epigenomic tools have the potential to identify novel biomarkers and better molecular targets to treat cancers. The purpose of this review is to discuss current and emerging epigenomic tools and to address how these new technologies may impact the future of cancer management

  1. NCBI Epigenomics: a new public resource for exploring epigenomic data sets.

    Science.gov (United States)

    Fingerman, Ian M; McDaniel, Lee; Zhang, Xuan; Ratzat, Walter; Hassan, Tarek; Jiang, Zhifang; Cohen, Robert F; Schuler, Gregory D

    2011-01-01

    The Epigenomics database at the National Center for Biotechnology Information (NCBI) is a new resource that has been created to serve as a comprehensive public resource for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). Epigenetics is the study of stable and heritable changes in gene expression that occur independently of the primary DNA sequence. Epigenetic mechanisms include post-translational modifications of histones, DNA methylation, chromatin conformation and non-coding RNAs. It has been observed that misregulation of epigenetic processes has been associated with human disease. We have constructed the new resource by selecting the subset of epigenetics-specific data from general-purpose archives, such as the Gene Expression Omnibus, and Sequence Read Archives, and then subjecting them to further review, annotation and reorganization. Raw data is processed and mapped to genomic coordinates to generate 'tracks' that are a visual representation of the data. These data tracks can be viewed using popular genome browsers or downloaded for local analysis. The Epigenomics resource also provides the user with a unique interface that allows for intuitive browsing and searching of data sets based on biological attributes. Currently, there are 69 studies, 337 samples and over 1100 data tracks from five well-studied species that are viewable and downloadable in Epigenomics.

  2. The International Human Epigenome Consortium

    DEFF Research Database (Denmark)

    Stunnenberg, Hendrik G; Hirst, Martin

    2016-01-01

    The International Human Epigenome Consortium (IHEC) coordinates the generation of a catalog of high-resolution reference epigenomes of major primary human cell types. The studies now presented (see the Cell Press IHEC web portal at http://www.cell.com/consortium/IHEC) highlight the coordinated...

  3. Epigenomics in environmental health

    Directory of Open Access Journals (Sweden)

    Carmen J Marsit

    2011-11-01

    Full Text Available This review considers the emerging relationships between environmental factors and epigenetic alterations and the application of genome-wide assessments to better define these relationships. First we will briefly cover epigenetic programming in development, one-carbon metabolism and exposures that may disrupt normal developmental programming of epigenetic states. In addition, because a large portion of epigenetic research has focused on cancer, we discuss exposures associated with carcinogenesis including asbestos, alcohol, radiation, arsenic, and air pollution. Research on other exposures that may affect epigenetic states such as endocrine disruptors is also described, and we also review the evidence for epigenetic alterations associated with aging that may reflect cumulative effects of exposures. From this evidence, we posit potential mechanisms by which exposures modify epigenetic states, noting that understanding the true effect of environmental exposures on the human epigenome will require additional research with appropriate epidemiologic studies and application of novel technologies. With a more comprehensive understanding of the affects of exposures on the epigenome, including consideration of genetic background, the prediction of the toxic potential of new compounds may be more readily achieved, and may lead to the development of more personalized disease prevention and treatment strategies.

  4. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. Chromatin and nuclear structure influence where and when DNA replication...... initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...... synthesis is perturbed, cells can suffer loss of both genome and epigenome integrity with severe consequences for the organism....

  5. Study on radiation-responsive epigenomes

    International Nuclear Information System (INIS)

    Kim, Jin Hong; Chung, Byung Yeop; Lee, Seung Sik; Moon, Yu Ran; Lee, Min Hee; Kim, Ji Hong

    2011-01-01

    The purpose of this project is development of world-class headspring techniques of biological science for application of plant genomes/epigenomes through study on radiation- responsive epigenomes and improvement of the national competitiveness in the field of fundamental technology for biological science and industry. Research scope includes 1) Investigation of radiation-responsive epigenomes and elucidation of their relation with phenotypes, 2) Elucidation of interaction and transcription control of epigenomes and epigenetic regulators using ionizing radiation (IR), 3) Investigation of epigenome-mediated traits in plant development, differentiation and antioxidant defense using IR, and 4) Development of application techniques of radiation-responsive epigenomes for eco-monitoring and molecular breeding. Main results are as follow: Setup of conditions for chromatin immunoprecipitation in irradiated plants: investigation of aberrations in DNA methylation after treatment with different IR: elucidation of responses of epigenetic regulators to gamma rays (GR): investigation of aberrations in GR-responsive epigenetic regulators at different developmental stages: elucidation of interactive aberrations of epigenomes and epigenetic regulators after treatment of GR: comparison of functional genomes after treatment of GR or H 2 O 2 : elucidation of relation of epigenomes with GR-induced delay in senescence: elucidation of relation of epigenomes with GR-induced aberrations in pigment metabolism: comparison of antioxidant defense in epigenetic mutants: investigation of senescence-associated changes in epigenomes: investigation of senescence-associated changes in epigenetic regulators: comparison of aberrations in epigenomes at different dose of GR for mutation

  6. Cancer Diagnosis Epigenomics Scientific Workflow Scheduling in the Cloud Computing Environment Using an Improved PSO Algorithm

    Science.gov (United States)

    N, Sadhasivam; R, Balamurugan; M, Pandi

    2018-01-27

    Objective: Epigenetic modifications involving DNA methylation and histone statud are responsible for the stable maintenance of cellular phenotypes. Abnormalities may be causally involved in cancer development and therefore could have diagnostic potential. The field of epigenomics refers to all epigenetic modifications implicated in control of gene expression, with a focus on better understanding of human biology in both normal and pathological states. Epigenomics scientific workflow is essentially a data processing pipeline to automate the execution of various genome sequencing operations or tasks. Cloud platform is a popular computing platform for deploying large scale epigenomics scientific workflow. Its dynamic environment provides various resources to scientific users on a pay-per-use billing model. Scheduling epigenomics scientific workflow tasks is a complicated problem in cloud platform. We here focused on application of an improved particle swam optimization (IPSO) algorithm for this purpose. Methods: The IPSO algorithm was applied to find suitable resources and allocate epigenomics tasks so that the total cost was minimized for detection of epigenetic abnormalities of potential application for cancer diagnosis. Result: The results showed that IPSO based task to resource mapping reduced total cost by 6.83 percent as compared to the traditional PSO algorithm. Conclusion: The results for various cancer diagnosis tasks showed that IPSO based task to resource mapping can achieve better costs when compared to PSO based mapping for epigenomics scientific application workflow. Creative Commons Attribution License

  7. Sleep Deprivation and the Epigenome.

    Science.gov (United States)

    Gaine, Marie E; Chatterjee, Snehajyoti; Abel, Ted

    2018-01-01

    Sleep deprivation disrupts the lives of millions of people every day and has a profound impact on the molecular biology of the brain. These effects begin as changes within a neuron, at the DNA and RNA level, and result in alterations in neuronal plasticity and dysregulation of many cognitive functions including learning and memory. The epigenome plays a critical role in regulating gene expression in the context of memory storage. In this review article, we begin by describing the effects of epigenetic alterations on the regulation of gene expression, focusing on the most common epigenetic mechanisms: (i) DNA methylation; (ii) histone modifications; and (iii) non-coding RNAs. We then discuss evidence suggesting that sleep loss impacts the epigenome and that these epigenetic alterations might mediate the changes in cognition seen following disruption of sleep. The link between sleep and the epigenome is only beginning to be elucidated, but clear evidence exists that epigenetic alterations occur following sleep deprivation. In the future, these changes to the epigenome could be utilized as biomarkers of sleep loss or as therapeutic targets for sleep-related disorders.

  8. Sleep Deprivation and the Epigenome

    Directory of Open Access Journals (Sweden)

    Marie E. Gaine

    2018-02-01

    Full Text Available Sleep deprivation disrupts the lives of millions of people every day and has a profound impact on the molecular biology of the brain. These effects begin as changes within a neuron, at the DNA and RNA level, and result in alterations in neuronal plasticity and dysregulation of many cognitive functions including learning and memory. The epigenome plays a critical role in regulating gene expression in the context of memory storage. In this review article, we begin by describing the effects of epigenetic alterations on the regulation of gene expression, focusing on the most common epigenetic mechanisms: (i DNA methylation; (ii histone modifications; and (iii non-coding RNAs. We then discuss evidence suggesting that sleep loss impacts the epigenome and that these epigenetic alterations might mediate the changes in cognition seen following disruption of sleep. The link between sleep and the epigenome is only beginning to be elucidated, but clear evidence exists that epigenetic alterations occur following sleep deprivation. In the future, these changes to the epigenome could be utilized as biomarkers of sleep loss or as therapeutic targets for sleep-related disorders.

  9. Sleep Deprivation and the Epigenome

    OpenAIRE

    Marie E. Gaine; Snehajyoti Chatterjee; Ted Abel

    2018-01-01

    Sleep deprivation disrupts the lives of millions of people every day and has a profound impact on the molecular biology of the brain. These effects begin as changes within a neuron, at the DNA and RNA level, and result in alterations in neuronal plasticity and dysregulation of many cognitive functions including learning and memory. The epigenome plays a critical role in regulating gene expression in the context of memory storage. In this review article, we begin by describing the effects of e...

  10. Mapping lichen distribution on the Antarctic Peninsula using remote sensing, lichen spectra and photographic documentation by citizen scientists

    Directory of Open Access Journals (Sweden)

    Paula Casanovas

    2015-10-01

    Full Text Available On the Antarctic Peninsula, lichens are the most diverse botanical component of the terrestrial ecosystem. However, detailed information on the distribution of lichens on the Antarctic Peninsula region is scarce, and the data available exhibit significant heterogeneity in sampling frequency and effort. Satellite remote sensing, in particular the use of the Normalized Difference Vegetation Index (NDVI, has facilitated determination of vegetation richness and cover distribution in some remote and otherwise inaccessible environments. However, it is known that using NDVI for the detection of vegetation can overlook the presence of lichens even if their land cover is extensive. We tested the use of known spectra of lichens in a matched filtering technique for the detection and mapping of lichen-covered land from remote sensing imagery on the Antarctic Peninsula, using data on lichen presence collected by citizen scientists and other non-specialists as ground truthing. Our results confirm that the use of this approach allows for the detection of lichen flora on the Antarctic Peninsula, showing an improvement over the use of NDVI alone for the mapping of flora in this area.

  11. Epigenomics

    Science.gov (United States)

    ... Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for Teachers Genomic ... part of the ENCODE (ENCyclopedia Of DNA Elements) project-which aims to ... National Human Genome Research Institute is funding researchers to make ...

  12. Applications of alignment-free methods in epigenomics.

    Science.gov (United States)

    Pinello, Luca; Lo Bosco, Giosuè; Yuan, Guo-Cheng

    2014-05-01

    Epigenetic mechanisms play an important role in the regulation of cell type-specific gene activities, yet how epigenetic patterns are established and maintained remains poorly understood. Recent studies have supported a role of DNA sequences in recruitment of epigenetic regulators. Alignment-free methods have been applied to identify distinct sequence features that are associated with epigenetic patterns and to predict epigenomic profiles. Here, we review recent advances in such applications, including the methods to map DNA sequence to feature space, sequence comparison and prediction models. Computational studies using these methods have provided important insights into the epigenetic regulatory mechanisms.

  13. Brain cancer genomics and epigenomics.

    Science.gov (United States)

    Archer, Tenley C; Sengupta, Soma; Pomeroy, Scott L

    2018-01-01

    Classically, brain cancers have been graded and diagnosed based on histology and risk stratified by clinical criteria. Recent advances in genomics and epigenomics have ushered in an era of defining cancers based on molecular criteria. These advances have increased our precision of identifying oncogenic driving events and, most importantly, increased our precision at predicting clinical outcome. For the first time in its history, the 2016 revision of the WHO Classification of Tumors of the Central Nervous System included molecular features as tumor classification criteria. Brain tumors can develop in the context of genetic cancer predisposition syndromes, such as Li-Fraumeni or Gorlin syndrome, but by far most commonly arise through the acquisition of somatic mutations and chromosome changes in the malignant cells. By taking a survey across this cancer landscape, certain themes emerge as being common events to drive cancer: DNA damage repair, genomic instability, mechanistic target of rapamycin pathway, sonic hedgehog pathway, hypoxia, and epigenetic dysfunction. Understanding these mechanisms is of paramount importance for improving targeted therapies, and for identifying the right patients for those therapies. Copyright © 2018 Elsevier B.V. All rights reserved.

  14. Epigenetics and Epigenomics of Plants.

    Science.gov (United States)

    Yadav, Chandra Bhan; Pandey, Garima; Muthamilarasan, Mehanathan; Prasad, Manoj

    2018-01-23

    The genetic material DNA in association with histone proteins forms the complex structure called chromatin, which is prone to undergo modification through certain epigenetic mechanisms including cytosine DNA methylation, histone modifications, and small RNA-mediated methylation. Alterations in chromatin structure lead to inaccessibility of genomic DNA to various regulatory proteins such as transcription factors, which eventually modulates gene expression. Advancements in high-throughput sequencing technologies have provided the opportunity to study the epigenetic mechanisms at genome-wide levels. Epigenomic studies using high-throughput technologies will widen the understanding of mechanisms as well as functions of regulatory pathways in plant genomes, which will further help in manipulating these pathways using genetic and biochemical approaches. This technology could be a potential research tool for displaying the systematic associations of genetic and epigenetic variations, especially in terms of cytosine methylation onto the genomic region in a specific cell or tissue. A comprehensive study of plant populations to correlate genotype to epigenotype and to phenotype, and also the study of methyl quantitative trait loci (QTL) or epiGWAS, is possible by using high-throughput sequencing methods, which will further accelerate molecular breeding programs for crop improvement. Graphical Abstract.

  15. Linking the Epigenome with Exposure Effects and ...

    Science.gov (United States)

    The epigenome is a dynamic mediator of gene expression that shapes the way that cells, tissues, and organisms respond to their environment. Initial studies in the emerging field of “toxicoepigenetics” have described either the impact of an environmental exposure on the epigenome or the association of epigenetic signatures with the onset or progression of disease: however, the majority of these pioneering studies examined the relationship between discrete epigenetic modifications and the effects of a single environmental factor. While these data provide critical blocks with which we construct our understanding of the role of the epigenome in susceptibility and disease, they are akin to individual letters in a complex alphabet that is used to compose the language of the epigenome. Advancing the use of epigenetic data to gain a more comprehensive understanding of the mechanisms underlying exposure effects, identify susceptible populations, and inform the next generation of risk management depends on our ability to integrate these data in a way that accounts for their cumulative impact on gene regulation. Here we will review current examples demonstrating associations between the epigenetic impacts of intrinsic factors, such as such as age, genetics, and sex, and environmental exposures shape the epigenome and susceptibility, to exposure effects and disease. We will also demonstrate how the “epigenetic seed and soil'' model can be used as a conceptua

  16. DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets.

    Science.gov (United States)

    Albrecht, Felipe; List, Markus; Bock, Christoph; Lengauer, Thomas

    2016-07-08

    Large amounts of epigenomic data are generated under the umbrella of the International Human Epigenome Consortium, which aims to establish 1000 reference epigenomes within the next few years. These data have the potential to unravel the complexity of epigenomic regulation. However, their effective use is hindered by the lack of flexible and easy-to-use methods for data retrieval. Extracting region sets of interest is a cumbersome task that involves several manual steps: identifying the relevant experiments, downloading the corresponding data files and filtering the region sets of interest. Here we present the DeepBlue Epigenomic Data Server, which streamlines epigenomic data analysis as well as software development. DeepBlue provides a comprehensive programmatic interface for finding, selecting, filtering, summarizing and downloading region sets. It contains data from four major epigenome projects, namely ENCODE, ROADMAP, BLUEPRINT and DEEP. DeepBlue comes with a user manual, examples and a well-documented application programming interface (API). The latter is accessed via the XML-RPC protocol supported by many programming languages. To demonstrate usage of the API and to enable convenient data retrieval for non-programmers, we offer an optional web interface. DeepBlue can be openly accessed at http://deepblue.mpi-inf.mpg.de. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Epigenomic programing: a future way to health?

    OpenAIRE

    Shenderov, Boris A.; Midtvedt, Tore

    2014-01-01

    It is now generally accepted that the ‘central genome dogma’ (i.e. a causal chain going from DNA to RNA to proteins and downstream to biological functions) should be replaced by the ‘fluid genome dogma’, that is, complex feed-forward and feed-back cycles that interconnect organism and environment by epigenomic programing – and reprograming – throughout life and at all levels, sometimes also down the generations. The epigenomic programing is the net sum of interactions derived from own metabol...

  18. The epigenomics of embryonic stem cell differentiation.

    Science.gov (United States)

    Kraushaar, Daniel C; Zhao, Keji

    2013-01-01

    Embryonic stem cells (ESCs) possess an open and highly dynamic chromatin landscape, which underlies their plasticity and ultimately maintains ESC pluripotency. The ESC epigenome must not only maintain the transcription of pluripotency-associated genes but must also, through gene priming, facilitate rapid and cell type-specific activation of developmental genes upon lineage commitment. Trans-generational inheritance ensures that the ESC chromatin state is stably transmitted from one generation to the next; yet at the same time, epigenetic marks are highly dynamic, reversible and responsive to extracellular cues. Once committed to differentiation, the ESC epigenome is remodeled and resolves into a more compact chromatin state. A thorough understanding of the role of chromatin modifiers in ESC fate and differentiation will be important if they are to be used for therapeutic purposes. Recent technical advances, particularly in next-generation sequencing technologies, have provided a genome-scale view of epigenetic marks and chromatin modifiers. More affordable and faster sequencing platforms have led to a comprehensive characterization of the ESC epigenome and epigenomes of differentiated cell types. In this review, we summarize and discuss the recent progress that has highlighted the central role of histone modifications, histone variants, DNA methylation and chromatin modifiers in ESC pluripotency and ESC fate. We provide a detailed and comprehensive discussion of genome-wide studies that are pertinent to our understanding of mammalian development.

  19. Keystone Symposia on Epigenomics and Chromatin Dynamics

    DEFF Research Database (Denmark)

    Ravnskjær, Kim

    2012-01-01

    Keystone Symposia kicked off the start of 2012 with two joint meetings on Epigenomics and Chromatin Dynamics and a star-studded list of speakers. Held in Keystone, CO, January 17-22, and organized by Steven Jacobsen and Steven Henikoff and by Bradley Cairns and Geneviève Almouzni, respectively...

  20. Rice epigenomics and epigenetics: challenges and opportunities.

    Science.gov (United States)

    Chen, Xiangsong; Zhou, Dao-Xiu

    2013-05-01

    During recent years rice genome-wide epigenomic information such as DNA methylation and histone modifications, which are important for genome activity has been accumulated. The function of a number of rice epigenetic regulators has been studied, many of which are found to be involved in a diverse range of developmental and stress-responsive pathways. Analysis of epigenetic variations among different rice varieties indicates that epigenetic modification may lead to inheritable phenotypic variation. Characterizing phenotypic consequences of rice epigenomic variations and the underlining chromatin mechanism and identifying epialleles related to important agronomic traits may provide novel strategies to enhance agronomically favorable traits and grain productivity in rice. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Epigenomics of cancer - emerging new concepts.

    Science.gov (United States)

    Hassler, Melanie R; Egger, Gerda

    2012-11-01

    The complexity of the mammalian genome is regulated by heritable epigenetic mechanisms, which provide the basis for differentiation, development and cellular homeostasis. These mechanisms act on the level of chromatin, by modifying DNA, histone proteins and nucleosome density/composition. During the last decade it became clear that cancer is defined by a variety of epigenetic changes, which occur in early stages of disease and parallel genetic mutations. With the advent of new technologies we are just starting to unravel the cancer epigenome and latest mechanistic findings provide the first clue as to how altered epigenetic patterns might occur in different cancers. Here we review latest findings on chromatin related mechanisms and hypothesize how their impairment might contribute to the altered epigenome of cancer cells. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  2. The Einstein Center for Epigenomics: studying the role of epigenomic dysregulation in human disease.

    Science.gov (United States)

    McLellan, Andrew S; Dubin, Robert A; Jing, Qiang; Maqbool, Shahina B; Olea, Raul; Westby, Gael; Broin, Pilib Ó; Fazzari, Melissa J; Zheng, Deyou; Suzuki, Masako; Greally, John M

    2009-10-01

    There is increasing interest in the role of epigenetic and transcriptional dysregulation in the pathogenesis of a range of human diseases, not just in the best-studied example of cancer. It is, however, quite difficult for an individual investigator to perform these studies, as they involve genome-wide molecular assays combined with sophisticated computational analytical approaches of very large datasets that may be generated from various resources and technologies. In 2008, the Albert Einstein College of Medicine in New York, USA established a Center for Epigenomics to facilitate the research programs of its investigators, providing shared resources for genome-wide assays and for data analysis. As a result, several avenues of research are now expanding, with cancer epigenomics being complemented by studies of the epigenomics of infectious disease and a neuroepigenomics program.

  3. dCas9 : A Versatile Tool For Epigenome Editing

    NARCIS (Netherlands)

    Brocken, D.J.W.; Tark-Dame, M.; Dame, R.T.

    2018-01-01

    The epigenome is a heritable layer of information not encoded in the DNA sequence of the genome, but in chemical modifications of DNA or histones. These chemical modifications, together with transcription factors, operate as spatiotemporal regulators of genome activity. Dissecting epigenome function

  4. From forensic epigenetics to forensic epigenomics: Broadening DNA investigative intelligence

    NARCIS (Netherlands)

    A. Vidaki (Athina); M.H. Kayser (Manfred)

    2017-01-01

    textabstractHuman genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment. We

  5. Robust Scientists

    DEFF Research Database (Denmark)

    Gorm Hansen, Birgitte

    their core i nterests, 2) developing a selfsupply of industry interests by becoming entrepreneurs and thus creating their own compliant industry partner and 3) balancing resources within a larger collective of researchers, thus countering changes in the influx of funding caused by shifts in political...... knowledge", Danish research policy seems to have helped develop politically and economically "robust scientists". Scientific robustness is acquired by way of three strategies: 1) tasting and discriminating between resources so as to avoid funding that erodes academic profiles and push scientists away from...

  6. The Epigenomic Landscape of Prokaryotes.

    Directory of Open Access Journals (Sweden)

    Matthew J Blow

    2016-02-01

    Full Text Available DNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. Here, we used single molecule, real-time sequencing to map DNA modifications including m6A, m4C, and m5C across the genomes of 230 diverse bacterial and archaeal species. We observed DNA methylation in nearly all (93% organisms examined, and identified a total of 834 distinct reproducibly methylated motifs. This data enabled annotation of the DNA binding specificities of 620 DNA Methyltransferases (MTases, doubling known specificities for previously hard to study Type I, IIG and III MTases, and revealing their extraordinary diversity. Strikingly, 48% of organisms harbor active Type II MTases with no apparent cognate restriction enzyme. These active 'orphan' MTases are present in diverse bacterial and archaeal phyla and show motif specificities and methylation patterns consistent with functions in gene regulation and DNA replication. Our results reveal the pervasive presence of DNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems.

  7. The sperm epigenome: implications for the embryo.

    Science.gov (United States)

    Gannon, John R; Emery, Benjamin R; Jenkins, Timothy G; Carrell, Douglas T

    2014-01-01

    Recent advances, including the human genome project and numerous studies of cancer and other diseases, have shown that the genetic code is not simply limited to the sequence of the four bases of DNA but also includes epigenetic programming, heritable changes that affect gene expression [Riggs A, Martinssen R, Russo V (2007) Introduction. In: Riggs A, Martinssen R, Russo V (eds) Epigenetics mechanisms of gene regulation. Cold Spring Harbor Press, New York]. The science of epigenetics is important in understanding many diseases and biological processes, including in identifying the causes of disease and better understanding the mechanisms by which the environment can affect gene expression [Carrell Fertil Steril 97 (2):267-274, 2012]. This chapter will focus on the epigenome of sperm and particularly highlight the potential role of the sperm epigenome in embryogenesis.The sperm epigenome is unique and highly specialized because of the unique nature and function of sperm and because of the diverse requirements for successful fertilization. Due to the need for motility, sperm chromatin must be compacted and highly organized. During spermiogenesis the chromatin is packaged tightly into the sperm head by the replacement of most histones with protamines. This allows for protection of the DNA from the hostile environment in the female reproductive tract. Remaining histones can have chemical modifications to the tails of the protein that either facilitate or repress gene transcription. Sperm, like embryonic stem cells, have a unique pattern of histone modifications that includes both activating and silencing marks in the promoters of genes associated with development. These bivalent marks, along with DNA hypomethylation, comprise a unique state in which the key genes are "poised" for possible activation in embryogenesis. Sperm epigenetic abnormalities have been linked with multiple diseases including male factor infertility and poor embryogenesis.

  8. Robust Scientists

    DEFF Research Database (Denmark)

    Gorm Hansen, Birgitte

    2012-01-01

    and adapting their i nterests to the needs of outside actors. However, when studying the concrete strategies of such successful scientists, matters seem a bit more complicated. Based on interviews with a plant biologist working in GMO the paper uses the biological concepts of field participants...

  9. Citizen Scientists

    Science.gov (United States)

    Bennett, Katherine

    2010-01-01

    The Harvard Forest Schoolyard Ecology Program provides teachers and students with the opportunity and materials to participate in regionally focused ecological studies under the guidance of a mentor scientist working on a similar study. The Harvard Forest is part of a national network of ecological research sites known as the Long Term Ecological…

  10. Epigenomic landscapes of retinal rods and cones

    Science.gov (United States)

    Mo, Alisa; Luo, Chongyuan; Davis, Fred P; Mukamel, Eran A; Henry, Gilbert L; Nery, Joseph R; Urich, Mark A; Picard, Serge; Lister, Ryan; Eddy, Sean R; Beer, Michael A; Ecker, Joseph R; Nathans, Jeremy

    2016-01-01

    Rod and cone photoreceptors are highly similar in many respects but they have important functional and molecular differences. Here, we investigate genome-wide patterns of DNA methylation and chromatin accessibility in mouse rods and cones and correlate differences in these features with gene expression, histone marks, transcription factor binding, and DNA sequence motifs. Loss of NR2E3 in rods shifts their epigenomes to a more cone-like state. The data further reveal wide differences in DNA methylation between retinal photoreceptors and brain neurons. Surprisingly, we also find a substantial fraction of DNA hypo-methylated regions in adult rods that are not in active chromatin. Many of these regions exhibit hallmarks of regulatory regions that were active earlier in neuronal development, suggesting that these regions could remain undermethylated due to the highly compact chromatin in mature rods. This work defines the epigenomic landscapes of rods and cones, revealing features relevant to photoreceptor development and function. DOI: http://dx.doi.org/10.7554/eLife.11613.001 PMID:26949250

  11. TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; referees: 1 approved, 2 approved with reservations

    Directory of Open Access Journals (Sweden)

    Tiago C. Silva

    2016-12-01

    Full Text Available Biotechnological advances in sequencing have led to an explosion of publicly available data via large international consortia such as The Cancer Genome Atlas (TCGA, The Encyclopedia of DNA Elements (ENCODE, and The NIH Roadmap Epigenomics Mapping Consortium (Roadmap. These projects have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high genomic resolution. The Bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. However, most packages are designed for specific data types (e.g. expression, epigenetics, genomics and there is no one comprehensive tool that provides a complete integrative analysis of the resources and data provided by all three public projects. A need to create an integration of these different analyses was recently proposed. In this workflow, we provide a series of biologically focused integrative analyses of different molecular data. We describe how to download, process and prepare TCGA data and by harnessing several key Bioconductor packages, we describe how to extract biologically meaningful genomic and epigenomic data. Using Roadmap and ENCODE data, we provide a work plan to identify biologically relevant functional epigenomic elements associated with cancer. To illustrate our workflow, we analyzed two types of brain tumors: low-grade glioma (LGG versus high-grade glioma (glioblastoma multiform or GBM. This workflow introduces the following Bioconductor packages: AnnotationHub, ChIPSeeker, ComplexHeatmap, pathview, ELMER, GAIA, MINET, RTCGAToolbox, TCGAbiolinks.

  12. From forensic epigenetics to forensic epigenomics: broadening DNA investigative intelligence.

    Science.gov (United States)

    Vidaki, Athina; Kayser, Manfred

    2017-12-21

    Human genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment. We envision future forensic applications of DNA methylation analysis that will broaden DNA-based forensic intelligence. Together with genetic prediction of appearance and biogeographic ancestry, epigenomic lifestyle prediction is expected to increase the ability of police to find unknown perpetrators of crime who are not identifiable using current forensic DNA profiling.

  13. Human DNA methylomes at base resolution show widespread epigenomic differences

    Science.gov (United States)

    Lister, Ryan; Pelizzola, Mattia; Dowen, Robert H.; Hawkins, R. David; Hon, Gary; Tonti-Filippini, Julian; Nery, Joseph R.; Lee, Leonard; Ye, Zhen; Ngo, Que-Minh; Edsall, Lee; Antosiewicz-Bourget, Jessica; Stewart, Ron; Ruotti, Victor; Millar, A. Harvey; Thomson, James A.; Ren, Bing; Ecker, Joseph R.

    2010-01-01

    Summary DNA cytosine methylation is a central epigenetic modification that plays essential roles in cellular processes including genome regulation, development and disease. Here we present the first genome-wide, single-base resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of mRNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA-protein interaction for several key regulatory factors. Widespread differences were identified in the composition and patterning of cytosine methylation between the two genomes. Nearly one-quarter of all methylation identified in embryonic stem cells was in a non-CG context, suggesting that they may utilize different methylation mechanisms to affect gene regulation. Methylation in non-CG contexts showed enrichment in gene bodies and depletion in protein binding sites and enhancers. Non-CG methylation disappeared upon induced differentiation of the embryonic stem cells, and was restored in induced pluripotent stem cells. We identified hundreds of differentially methylated regions proximal to genes involved in pluripotency and differentiation, and widespread reduced methylation levels in fibroblasts associated with lower transcriptional activity. These reference epigenomes provide a foundation for future studies exploring this key epigenetic modification in human disease and development. PMID:19829295

  14. Sustainable Scientists

    Energy Technology Data Exchange (ETDEWEB)

    Mills, Evan

    2008-12-31

    Scientists are front and center in quantifying and solving environmental problems. Yet, as a spate of recent news articles in scientific journals point out, much can be done to enhance sustainability within the scientific enterprise itself, particularly by trimming the energy use associated with research facilities and the equipment therein (i,ii,iii, iv). Sponsors of research unwittingly spend on the order of $10 billion each year on energy in the U.S. alone, and the underlying inefficiencies drain funds from the research enterprise while causing 80 MT CO2-equivalent greenhouse-gas emissions (see Box). These are significant sums considering the opportunity costs in terms of the amount of additional research that could be funded and emissions that could be reduced if the underlying energy was used more efficiently. By following commercially proven best practices in facility design and operation, scientists--and the sponsors of science--can cost-effectively halve these costs, while doing their part to put society on alow-carbon diet.

  15. Nutritional epigenomics: a portal to disease prevention.

    Science.gov (United States)

    Choi, Sang-Woon; Claycombe, Kate J; Martinez, J Alfredo; Friso, Simonetta; Schalinske, Kevin L

    2013-09-01

    Epigenetics can be defined as inheritable and reversible phenomena that affect gene expression without altering the underlying base pair sequence. Epigenomics is the study of genome-wide epigenetic modifications. Because gene expression changes are critical in both normal development and disease progression, epigenetics is widely applicable to many aspects of biological research. The influences of nutrients and bioactive food components on epigenetic phenomena such as DNA methylation and various types of histone modifications have been extensively investigated. Because an individual's epigenetic patterns are established during early gestation and are changed and personalized by environmental factors during our lifetime, epigenetic mechanisms are quite important in the development of transgenerational and adult obesity as well as in the development of diabetes mellitus. Aging and cancer demonstrate profound genome-wide DNA methylation changes, suggesting that nutrition may affect the aging process and cancer development through epigenetic mechanisms.

  16. Epigenomic Adaptation to Low Dose Radiation

    Energy Technology Data Exchange (ETDEWEB)

    Gould, Michael N. [Univ. of Wisconsin, Madison, WI (United States)

    2015-06-30

    The overall hypothesis of this grant application is that the adaptive responses elicited by low dose ionizing radiation (LDIR) result in part from heritable DNA methylation changes in the epigenome. In the final budget period at the University of Wisconsin-Madison, we will specifically address this hypothesis by determining if the epigenetically labile, differentially methylated regions (DMRs) that regulate parental-specific expression of imprinted genes are deregulated in agouti mice by low dose radiation exposure during gestation. This information is particularly important to ascertain given the 1) increased human exposure to medical sources of radiation; 2) increased number of people predicted to live and work in space; and 3) enhanced citizen concern about radiation exposure from nuclear power plant accidents and terrorist ‘dirty bombs.’

  17. From forensic epigenetics to forensic epigenomics: Broadening DNA investigative intelligence

    OpenAIRE

    Vidaki, Athina; Kayser, Manfred

    2017-01-01

    textabstractHuman genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment. We envision future forensic applications of DNA methylation analysis that will broaden DNA-based forensic intelligence. Together with genetic prediction of appearance and biogeographic ancestry, epigenomi...

  18. Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells

    Science.gov (United States)

    Szulwach, Keith E.; Li, Xuekun; Li, Yujing; Song, Chun-Xiao; Han, Ji Woong; Kim, SangSung; Namburi, Sandeep; Hermetz, Karen; Kim, Julie J.; Rudd, M. Katharine; Yoon, Young-Sup; Ren, Bing; He, Chuan; Jin, Peng

    2011-01-01

    Covalent modification of DNA distinguishes cellular identities and is crucial for regulating the pluripotency and differentiation of embryonic stem (ES) cells. The recent demonstration that 5-methylcytosine (5-mC) may be further modified to 5-hydroxymethylcytosine (5-hmC) in ES cells has revealed a novel regulatory paradigm to modulate the epigenetic landscape of pluripotency. To understand the role of 5-hmC in the epigenomic landscape of pluripotent cells, here we profile the genome-wide 5-hmC distribution and correlate it with the genomic profiles of 11 diverse histone modifications and six transcription factors in human ES cells. By integrating genomic 5-hmC signals with maps of histone enrichment, we link particular pluripotency-associated chromatin contexts with 5-hmC. Intriguingly, through additional correlations with defined chromatin signatures at promoter and enhancer subtypes, we show distinct enrichment of 5-hmC at enhancers marked with H3K4me1 and H3K27ac. These results suggest potential role(s) for 5-hmC in the regulation of specific promoters and enhancers. In addition, our results provide a detailed epigenomic map of 5-hmC from which to pursue future functional studies on the diverse regulatory roles associated with 5-hmC. PMID:21731508

  19. Genomics and epigenomics of the human glycome.

    Science.gov (United States)

    Zoldoš, Vlatka; Novokmet, Mislav; Bečeheli, Ivona; Lauc, Gordan

    2013-01-01

    The majority of all proteins are glycosylated and glycans have numerous important structural, functional and regulatory roles in various physiological processes. While structure of the polypeptide part of a glycoprotein is defined by the sequence of nucleotides in the corresponding gene, structure of a glycan part results from dynamic interactions between hundreds of genes, their protein products and environmental factors. The composition of the glycome attached to an individual protein, or to a complex mixture of proteins, like human plasma, is stable within an individual, but very variable between individuals. This variability stems from numerous common genetic polymorphisms reflecting in changes in the complex biosynthetic pathway of glycans, but also from the interaction with the environment. Environment can affect glycan biosynthesis at the level of substrate availability, regulation of enzyme activity and/or hormonal signals, but also through gene-environment interactions. Epigenetics provides a molecular basis how the environment can modify phenotype of an individual. The epigenetic information (DNA methylation pattern and histone code) is especially vulnerable to environmental effects in the early intrauterine and neo-natal development and many common late-onset diseases take root already at that time. The evidences showing the link between epigenetics and glycosylation are accumulating. Recent progress in high-throughput glycomics, genomics and epigenomics enabled first epidemiological and genome-wide association studies of the glycome, which are presented in this mini-review.

  20. Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs

    Science.gov (United States)

    Amin, Viren; Harris, R. Alan; Onuchic, Vitor; Jackson, Andrew R.; Charnecki, Tim; Paithankar, Sameer; Lakshmi Subramanian, Sai; Riehle, Kevin; Coarfa, Cristian; Milosavljevic, Aleksandar

    2015-01-01

    Tissue-specific expression of lincRNAs suggests developmental and cell-type-specific functions, yet tissue specificity was established for only a small fraction of lincRNAs. Here, by analysing 111 reference epigenomes from the NIH Roadmap Epigenomics project, we determine tissue-specific epigenetic regulation for 3,753 (69% examined) lincRNAs, with 54% active in one of the 14 cell/tissue clusters and an additional 15% in two or three clusters. A larger fraction of lincRNA TSSs is marked in a tissue-specific manner by H3K4me1 than by H3K4me3. The tissue-specific lincRNAs are strongly linked to tissue-specific pathways and undergo distinct chromatin state transitions during cellular differentiation. Polycomb-regulated lincRNAs reside in the bivalent state in embryonic stem cells and many of them undergo H3K27me3-mediated silencing at early stages of differentiation. The exquisitely tissue-specific epigenetic regulation of lincRNAs and the assignment of a majority of them to specific tissue types will inform future studies of this newly discovered class of genes. PMID:25691256

  1. A glutamatergic network mediates lithium response in bipolar disorder as defined by epigenome pathway analysis.

    Science.gov (United States)

    Higgins, Gerald A; Allyn-Feuer, Ari; Barbour, Edward; Athey, Brian D

    2015-01-01

    A regulatory network in the human brain mediating lithium response in bipolar patients was revealed by analysis of functional SNPs from genome-wide association studies (GWAS) and published gene association studies, followed by epigenome mapping. An initial set of 23,312 SNPs in linkage disequilibrium with lead SNPs, and sub-threshold GWAS SNPs rescued by pathway analysis, were studied in the same populations. These were assessed using our workflow and annotation by the epigenome roadmap consortium. Twenty-seven percent of 802 SNPs that were associated with lithium response (13 published studies gene association studies and two GWAS) were shared in common with 1281 SNPs from 18 GWAS examining psychiatric disorders and adverse events associated with lithium treatment. Nineteen SNPs were annotated as active regulatory elements such as enhancers and promoters in a tissue-specific manner. They were located within noncoding regions of ten genes: ANK3, ARNTL, CACNA1C, CACNG2, CDKN1A, CREB1, GRIA2, GSK3B, NR1D1 and SLC1A2. Following gene set enrichment and pathway analysis, these genes were found to be significantly associated (p = 10(-27); Fisher exact test) with an AMPA2 glutamate receptor network in human brain. Our workflow results showed concordance with annotation of regulatory elements from the epigenome roadmap. Analysis of cognate mRNA and enhancer RNA exhibited patterns consistent with an integrated pathway in human brain. This pharmacoepigenomic regulatory pathway is located in the same brain regions that exhibit tissue volume loss in bipolar disorder. Although in silico analysis requires biological validation, the approach provides value for identification of candidate variants that may be used in pharmacogenomic testing to identify bipolar patients likely to respond to lithium.

  2. Integrating Epigenomics into the Understanding of Biomedical Insight.

    Science.gov (United States)

    Han, Yixing; He, Ximiao

    2016-01-01

    Epigenetics is one of the most rapidly expanding fields in biomedical research, and the popularity of the high-throughput next-generation sequencing (NGS) highlights the accelerating speed of epigenomics discovery over the past decade. Epigenetics studies the heritable phenotypes resulting from chromatin changes but without alteration on DNA sequence. Epigenetic factors and their interactive network regulate almost all of the fundamental biological procedures, and incorrect epigenetic information may lead to complex diseases. A comprehensive understanding of epigenetic mechanisms, their interactions, and alterations in health and diseases genome widely has become a priority in biological research. Bioinformatics is expected to make a remarkable contribution for this purpose, especially in processing and interpreting the large-scale NGS datasets. In this review, we introduce the epigenetics pioneering achievements in health status and complex diseases; next, we give a systematic review of the epigenomics data generation, summarize public resources and integrative analysis approaches, and finally outline the challenges and future directions in computational epigenomics.

  3. Cancer chemoprevention by targeting the epigenome.

    Science.gov (United States)

    Huang, Joseph; Plass, Christoph; Gerhauser, Clarissa

    2011-12-01

    The term "epigenetics" refers to modifications in gene expression caused by heritable, but potentially reversible, changes in DNA methylation and chromatin structure. Given the fact that epigenetic modifications occur early in carcinogenesis and represent potentially initiating events in cancer development, they have been identified as promising new targets for prevention strategies. The present review will give a comprehensive overview of the current literature on chemopreventive agents and their influence on major epigenetic mechanisms, that is DNA methylation, histone acetylation and methylation, and microRNAs, both in vitro and in rodent and human studies, taking into consideration specific mechanisms of action, target sites, concentrations, methods used for analysis, and outcome. Chemopreventive agents with reported mechanisms targeting the epigenome include micronutrients (folate, selenium, retinoic acid, Vit. E), butyrate, polyphenols (from green tea, apples, coffee, and other dietary sources), genistein and soy isoflavones, parthenolide, curcumin, ellagitannin, indol-3-carbinol (I3C) and diindolylmethane (DIM), mahanine, nordihydroguaiaretic acid (NDGA), lycopene, sulfur-containing compounds from Allium and cruciferous vegetables (sulforaphane, phenylethyl isothiocyanate (PEITC), phenylhexyl isothiocyanate (PHI), diallyldisulfide (DADS), allyl mercaptan (AM)), antibiotics (mithramycin A, apicidin), pharmacological agents (celecoxib, DFMO, 5-aza-2'-deoxycytidine and zebularine), compounds affecting sirtuin activity (resveratrol, dihydrocoumarin, cambinol), inhibitors of histone acetyl transferases (anacardic acid, garcinol, ursodeoxycholic acid), and relatively unexplored modulators of histone lysine methylation (chaetocin, polyamine analogues, n-3 polyunsaturated fatty acids). Their effects on global DNA methylation, tumor suppressor genes silenced by promoter methylation, histone modifications, and miRNAs deregulated during carcinogenesis have potential

  4. Epigenome-Wide Association Study Identifies Cardiac Gene Patterning and a Novel Class of Biomarkers for Heart Failure.

    Science.gov (United States)

    Meder, Benjamin; Haas, Jan; Sedaghat-Hamedani, Farbod; Kayvanpour, Elham; Frese, Karen; Lai, Alan; Nietsch, Rouven; Scheiner, Christina; Mester, Stefan; Bordalo, Diana Martins; Amr, Ali; Dietrich, Carsten; Pils, Dietmar; Siede, Dominik; Hund, Hauke; Bauer, Andrea; Holzer, Daniel Benjamin; Ruhparwar, Arjang; Mueller-Hennessen, Matthias; Weichenhan, Dieter; Plass, Christoph; Weis, Tanja; Backs, Johannes; Wuerstle, Maximilian; Keller, Andreas; Katus, Hugo A; Posch, Andreas E

    2017-10-17

    Biochemical DNA modification resembles a crucial regulatory layer among genetic information, environmental factors, and the transcriptome. To identify epigenetic susceptibility regions and novel biomarkers linked to myocardial dysfunction and heart failure, we performed the first multi-omics study in myocardial tissue and blood of patients with dilated cardiomyopathy and controls. Infinium human methylation 450 was used for high-density epigenome-wide mapping of DNA methylation in left-ventricular biopsies and whole peripheral blood of living probands. RNA deep sequencing was performed on the same samples in parallel. Whole-genome sequencing of all patients allowed exclusion of promiscuous genotype-induced methylation calls. In the screening stage, we detected 59 epigenetic loci that are significantly associated with dilated cardiomyopathy (false discovery corrected P ≤0.05), with 3 of them reaching epigenome-wide significance at P ≤5×10 -8 . Twenty-seven (46%) of these loci could be replicated in independent cohorts, underlining the role of epigenetic regulation of key cardiac transcription regulators. Using a staged multi-omics study design, we link a subset of 517 epigenetic loci with dilated cardiomyopathy and cardiac gene expression. Furthermore, we identified distinct epigenetic methylation patterns that are conserved across tissues, rendering these CpGs novel epigenetic biomarkers for heart failure. The present study provides to our knowledge the first epigenome-wide association study in living patients with heart failure using a multi-omics approach. © 2017 American Heart Association, Inc.

  5. Finding a new continent versus mapping all the rivers: Recognition, ownership, and the scientific epistemological development of practicing scientists and engineers

    Science.gov (United States)

    Verdan, Andrea Marie

    Maintaining our nation's standing as a leader of innovative and premier science and engineering research requires that those on the trajectory of these careers receive both rigorous and exceptional training. In addition to educating students in the content knowledge of these disciplines, it is also necessary to train them in the professional skills associated with being competent and conscientious scientists and engineers. In the attempts to understand the best strategies to teach these skills, research during the past few decades has shown a steadily increasing interest in improving the scientific literacy of students in science and engineering disciplines. Researchers agree that fostering this literacy---particularly with respect to understanding the nature of science, i.e., scientific epistemology---is an important component in developing students' abilities to become successful practitioners of science and engineering. This research was motivated by the need to further elucidate the formative experiences that contribute to science and engineering faculty members' personal epistemologies of science. To examine the development of these epistemologies, a phenomenographical study was designed to elucidate academic scientists' and engineers' understandings of contributions, collaborations, and credit assignment. The results and inductive, grounded-theory analysis of interviews with faculty members in the College of Engineering and Science at a large, southeastern institution revealed a model of scientific epistemological development and its possible ties to professional identity development. This model can help inform changes in mentorship and training practices to better prepare students to manage the challenges posed by being scientists and engineers in the 21st-century.

  6. Epigenome-Wide Association Study of Tic Disorders

    NARCIS (Netherlands)

    Rodrigues Zilhao Nogueira, N.; Padmanabhuni, S.S.; Pagliaroli, L.; Barta, C.; Smit, D.J.A.; Cath, D.C.; Nivard, M.G.; Baselmans, B.M.L.; van Dongen, J.; Paschou, P.; Boomsma, D.I.

    2015-01-01

    Tic disorders are moderately heritable common psychiatric disorders that can be highly troubling, both in childhood and in adulthood. In this study, we report results obtained in the first epigenome-wide association study (EWAS) of tic disorders. The subjects are participants in surveys at the

  7. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... search for current job openings visit HHS USAJobs Home >> NEI for Kids >> Ask a Scientist Video Series ... can see clearly from 25 feet away. NEI Home Contact Us A-Z Site Map NEI on ...

  8. How Scientists Develop Competence in Visual Communication

    Science.gov (United States)

    Ostergren, Marilyn

    2013-01-01

    Visuals (maps, charts, diagrams and illustrations) are an important tool for communication in most scientific disciplines, which means that scientists benefit from having strong visual communication skills. This dissertation examines the nature of competence in visual communication and the means by which scientists acquire this competence. This…

  9. Plants regenerated from tissue culture contain stable epigenome changes in rice.

    Science.gov (United States)

    Stroud, Hume; Ding, Bo; Simon, Stacey A; Feng, Suhua; Bellizzi, Maria; Pellegrini, Matteo; Wang, Guo-Liang; Meyers, Blake C; Jacobsen, Steven E

    2013-03-19

    Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several regenerated rice lines. We found that all tested regenerated plants had significant losses of methylation compared to non-regenerated plants. Loss of methylation was largely stable across generations, and certain sites in the genome were particularly susceptible to loss of methylation. Loss of methylation at promoters was associated with deregulated expression of protein-coding genes. Analyses of callus and untransformed plants regenerated from callus indicated that loss of methylation is stochastically induced at the tissue culture step. These changes in methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest phenotypic variability. DOI:http://dx.doi.org/10.7554/eLife.00354.001.

  10. Toward understanding the evolution of vertebrate gene regulatory networks: comparative genomics and epigenomic approaches.

    Science.gov (United States)

    Martinez-Morales, Juan R

    2016-07-01

    Vertebrates, as most animal phyla, originated >500 million years ago during the Cambrian explosion, and progressively radiated into the extant classes. Inferring the evolutionary history of the group requires understanding the architecture of the developmental programs that constrain the vertebrate anatomy. Here, I review recent comparative genomic and epigenomic studies, based on ChIP-seq and chromatin accessibility, which focus on the identification of functionally equivalent cis-regulatory modules among species. This pioneer work, primarily centered in the mammalian lineage, has set the groundwork for further studies in representative vertebrate and chordate species. Mapping of active regulatory regions across lineages will shed new light on the evolutionary forces stabilizing ancestral developmental programs, as well as allowing their variation to sustain morphological adaptations on the inherited vertebrate body plan. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  11. Epigenome-wide association study of chronic obstructive pulmonary disease and lung function in Koreans.

    Science.gov (United States)

    Lee, Mi Kyeong; Hong, Yoonki; Kim, Sun-Young; Kim, Woo Jin; London, Stephanie J

    2017-07-01

    To identify differentially methylated probes (DMPs) and regions (DMRs) in relation to chronic obstructive pulmonary disease (COPD) and lung function traits. We performed an epigenome-wide association study of COPD and spirometric parameters, including forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC, in blood DNA using the Infinium HumanMethylation450 (n = 100, a Korean COPD cohort). We found one significant DMP (cg03559389, DIP2C) and 104 significant DMRs after multiple-testing correction. Of these, 34 DMRs mapped to genes differential expressed with respect to the same trait. Five of the genes were associated with more than two traits: CTU2, USP36, ZNF516, KLK10 and CPT1B. We identified novel differential methylation loci related to COPD and lung function in blood DNA in Koreans and confirmed previous findings in non-Asians. Epigenetic modification could contribute to the etiology of these phenotypes.

  12. Advances in epigenetics and epigenomics for neurodegenerative diseases.

    Science.gov (United States)

    Qureshi, Irfan A; Mehler, Mark F

    2011-10-01

    In the post-genomic era, epigenetic factors-literally those that are "over" or "above" genetic ones and responsible for controlling the expression and function of genes-have emerged as important mediators of development and aging; gene-gene and gene-environmental interactions; and the pathophysiology of complex disease states. Here, we provide a brief overview of the major epigenetic mechanisms (ie, DNA methylation, histone modifications and chromatin remodeling, and non-coding RNA regulation). We highlight the nearly ubiquitous profiles of epigenetic dysregulation that have been found in Alzheimer's and other neurodegenerative diseases. We also review innovative methods and technologies that enable the characterization of individual epigenetic modifications and more widespread epigenomic states at high resolution. We conclude that, together with complementary genetic, genomic, and related approaches, interrogating epigenetic and epigenomic profiles in neurodegenerative diseases represent important and increasingly practical strategies for advancing our understanding of and the diagnosis and treatment of these disorders.

  13. Epigenetic diet: impact on the epigenome and cancer.

    Science.gov (United States)

    Hardy, Tabitha M; Tollefsbol, Trygve O

    2011-08-01

    A number of bioactive dietary components are of particular interest in the field of epigenetics. Many of these compounds display anticancer properties and may play a role in cancer prevention. Numerous studies suggest that a number of nutritional compounds have epigenetic targets in cancer cells. Importantly, emerging evidence strongly suggests that consumption of dietary agents can alter normal epigenetic states as well as reverse abnormal gene activation or silencing. Epigenetic modifications induced by bioactive dietary compounds are thought to be beneficial. Substantial evidence is mounting proclaiming that commonly consumed bioactive dietary factors act to modify the epigenome and may be incorporated into an 'epigenetic diet'. Bioactive nutritional components of an epigenetic diet may be incorporated into one's regular dietary regimen and used therapeutically for medicinal or chemopreventive purposes. This article will primarily focus on dietary factors that have been demonstrated to influence the epigenome and that may be used in conjunction with other cancer prevention and chemotherapeutic therapies.

  14. Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions.

    Directory of Open Access Journals (Sweden)

    Chieh-Chun Chen

    Full Text Available Despite explosive growth in genomic datasets, the methods for studying epigenomic mechanisms of gene regulation remain primitive. Here we present a model-based approach to systematically analyze the epigenomic functions in modulating transcription factor-DNA binding. Based on the first principles of statistical mechanics, this model considers the interactions between epigenomic modifications and a cis-regulatory module, which contains multiple binding sites arranged in any configurations. We compiled a comprehensive epigenomic dataset in mouse embryonic stem (mES cells, including DNA methylation (MeDIP-seq and MRE-seq, DNA hydroxymethylation (5-hmC-seq, and histone modifications (ChIP-seq. We discovered correlations of transcription factors (TFs for specific combinations of epigenomic modifications, which we term epigenomic motifs. Epigenomic motifs explained why some TFs appeared to have different DNA binding motifs derived from in vivo (ChIP-seq and in vitro experiments. Theoretical analyses suggested that the epigenome can modulate transcriptional noise and boost the cooperativity of weak TF binding sites. ChIP-seq data suggested that epigenomic boost of binding affinities in weak TF binding sites can function in mES cells. We showed in theory that the epigenome should suppress the TF binding differences on SNP-containing binding sites in two people. Using personal data, we identified strong associations between H3K4me2/H3K9ac and the degree of personal differences in NFκB binding in SNP-containing binding sites, which may explain why some SNPs introduce much smaller personal variations on TF binding than other SNPs. In summary, this model presents a powerful approach to analyze the functions of epigenomic modifications. This model was implemented into an open source program APEG (Affinity Prediction by Epigenome and Genome, http://systemsbio.ucsd.edu/apeg.

  15. Targeting the epigenome with bioactive food components for cancer prevention.

    Science.gov (United States)

    Ong, Thomas Prates; Moreno, Fernando Salvador; Ross, Sharon Ann

    2011-01-01

    Epigenetic processes participate in cancer development and likely influence cancer prevention. Global DNA hypomethylation, gene promoter hypermethylation and aberrant histone post-translational modifications are hallmarks of neoplastic cells which have been associated with genomic instability and altered gene expression. Because epigenetic deregulation occurs early in carcinogenesis and is potentially reversible, intervention strategies targeting the epigenome have been proposed for cancer prevention. Bioactive food components (BFCs) with anticancer potential, including folate, polyphenols, selenium, retinoids, fatty acids, isothiocyanates and allyl compounds, influence DNA methylation and histone modification processes. Such activities have been shown to affect the expression of genes involved in cell proliferation, death and differentiation that are frequently altered in cancer. Although the epigenome represents a promising target for cancer prevention with BFCs, few studies have addressed the influence of dietary components on these mechanisms in vivo, particularly on the phenotype of humans, and thus the exact mechanisms whereby diet mediates an effect on cancer prevention remains unclear. Primary factors that should be elucidated include the effective doses and dose timing of BFCs to attain epigenetic effects. Because diet-epigenome interactions are likely to occur in utero, the impact of early-life nutrition on cancer risk programming should be further investigated. Copyright © 2012 S. Karger AG, Basel.

  16. Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain

    Directory of Open Access Journals (Sweden)

    Chongyuan Luo

    2016-12-01

    Full Text Available Organoids derived from human pluripotent stem cells recapitulate the early three-dimensional organization of the human brain, but whether they establish the epigenomic and transcriptional programs essential for brain development is unknown. We compared epigenomic and regulatory features in cerebral organoids and human fetal brain, using genome-wide, base resolution DNA methylome and transcriptome sequencing. Transcriptomic dynamics in organoids faithfully modeled gene expression trajectories in early-to-mid human fetal brains. We found that early non-CG methylation accumulation at super-enhancers in both fetal brain and organoids marks forthcoming transcriptional repression in the fully developed brain. Demethylated regions (74% of 35,627 identified during organoid differentiation overlapped with fetal brain regulatory elements. Interestingly, pericentromeric repeats showed widespread demethylation in multiple types of in vitro human neural differentiation models but not in fetal brain. Our study reveals that organoids recapitulate many epigenomic features of mid-fetal human brain and also identified novel non-CG methylation signatures of brain development.

  17. Next-generation technologies and data analytical approaches for epigenomics.

    Science.gov (United States)

    Mensaert, Klaas; Denil, Simon; Trooskens, Geert; Van Criekinge, Wim; Thas, Olivier; De Meyer, Tim

    2014-04-01

    Epigenetics refers to the collection of heritable features that modulate the genome-environment interaction without being encoded in the actual DNA sequence. While being mitotically and sometimes even meiotically transmitted, epigenetic traits often demonstrate extensive flexibility. This allows cells to acquire diverse gene expression patterns during differentiation, but also to adapt to a changing environment. However, epigenetic alterations are not always beneficial to the organism, as they are, for example, frequently identified in human diseases such as cancer. Accurate and cost-efficient genome-scale profiling of epigenetic features is thus of major importance to pinpoint these "epimutations," for example, to monitor the epigenetic impact of environmental exposure. Over the last decade, the field of epigenetics has been revolutionized by several innovative "epigenomics" technologies exactly addressing this need. In this review, we discuss and compare widely used next-generation methods to assess DNA methylation and hydroxymethylation, noncoding RNA expression, histone modifications, and nucleosome positioning. Although recent methods are typically based on "second-generation" sequencing, we also pay attention to still commonly used array- and PCR-based methods, and look forward to the additional advantages of single-molecule sequencing. As the current bottleneck in epigenomics research is the analysis rather than generation of data, the basic difficulties and problem-solving strategies regarding data preprocessing and statistical analysis are introduced for the different technologies. Finally, we also consider the complications associated with epigenomic studies of species with yet unsequenced genomes and possible solutions. Copyright © 2013 Wiley Periodicals, Inc.

  18. Scientists must speak

    National Research Council Canada - National Science Library

    Walters, D. Eric; Walters, Gale Climenson

    2011-01-01

    .... Scientists Must Speak: Bringing Presentations to Life helps readers do just that. At some point in their careers, the majority of scientists have to stand up in front of an inquisitive audience or board and present information...

  19. The scientist lady

    Indian Academy of Sciences (India)

    Lawrence

    The scientist lady. Kamala Sohonie. (by Vasumati Dhuru). 9. Kamala Sohonie was a quiet, unassuming person. A woman of few words. To look at her one would think that the stream of her ... not think a woman scientist, to be research material! Kamala ... many distinguished scientists among the list of students she trained.

  20. From Students to Scientists

    Science.gov (United States)

    Ho-Shing, Olivia

    2017-01-01

    In his book "Letters to a Young Scientist," renowned biologist Edward O. Wilson recounted his own coming-of-age story as a scientist, and distilled the motivating qualities of science down to curiosity and creativity. Individuals become scientists when they are curious about a phenomenon in the world around them and ask about the real…

  1. Scientists: Engage the Public!

    Science.gov (United States)

    Shugart, Erika C; Racaniello, Vincent R

    2015-12-22

    Scientists must communicate about science with public audiences to promote an understanding of complex issues that we face in our technologically advanced society. Some scientists may be concerned about a social stigma or "Sagan effect" associated with participating in public communication. Recent research in the social sciences indicates that public communication by scientists is not a niche activity but is widely done and can be beneficial to a scientist's career. There are a variety of approaches that scientists can take to become active in science communication. Copyright © 2015 Shugart and Racaniello.

  2. Inferring Past Environments from Ancient Epigenomes.

    Science.gov (United States)

    Gokhman, David; Malul, Anat; Carmel, Liran

    2017-10-01

    Analyzing the conditions in which past individuals lived is key to understanding the environments and cultural transitions to which humans had to adapt. Here, we suggest a methodology to probe into past environments, using reconstructed premortem DNA methylation maps of ancient individuals. We review a large body of research showing that differential DNA methylation is associated with changes in various external and internal factors, and propose that loci whose DNA methylation level is environmentally responsive could serve as markers to infer about ancient daily life, diseases, nutrition, exposure to toxins, and more. We demonstrate this approach by showing that hunger-related DNA methylation changes are found in ancient hunter-gatherers. The strategy we present here opens a window to reconstruct previously inaccessible aspects of the lives of past individuals. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  3. Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning.

    Science.gov (United States)

    Dozmorov, Mikhail G

    2017-10-15

    One of the goals of functional genomics is to understand the regulatory implications of experimentally obtained genomic regions of interest (ROIs). Most sequencing technologies now generate ROIs distributed across the whole genome. The interpretation of these genome-wide ROIs represents a challenge as the majority of them lie outside of functionally well-defined protein coding regions. Recent efforts by the members of the International Human Epigenome Consortium have generated volumes of functional/regulatory data (reference epigenomic datasets), effectively annotating the genome with epigenomic properties. Consequently, a wide variety of computational tools has been developed utilizing these epigenomic datasets for the interpretation of genomic data. The purpose of this review is to provide a structured overview of practical solutions for the interpretation of ROIs with the help of epigenomic data. Starting with epigenomic enrichment analysis, we discuss leading tools and machine learning methods utilizing epigenomic and 3D genome structure data. The hierarchy of tools and methods reviewed here presents a practical guide for the interpretation of genome-wide ROIs within an epigenomic context. mikhail.dozmorov@vcuhealth.org. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  4. Epigenome-wide association of DNA methylation in whole blood with bone mineral density

    DEFF Research Database (Denmark)

    Morris, John A; Tsai, Pei-Chien; Joehanes, Roby

    2017-01-01

    Genetic and environmental determinants of skeletal phenotypes such as bone mineral density (BMD) may converge through the epigenome, providing a tool to better understand osteoporosis pathophysiology. As the epigenetics of BMD have been largely unexplored in humans, we performed an epigenome wide...

  5. Linking the Epigenome with Exposure Effects and Susceptibility: The Epigenetic Seed and Soil Model.

    Science.gov (United States)

    The epigenome is a dynamic mediator of gene expression that shapes the way that cells, tissues, and organisms respond to their environment. Initial studies in the emerging field of “toxicoepigenetics” have described either the impact of an environmental exposure on the epigenome...

  6. CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.

    Science.gov (United States)

    Klann, Tyler S; Black, Joshua B; Chellappan, Malathi; Safi, Alexias; Song, Lingyun; Hilton, Isaac B; Crawford, Gregory E; Reddy, Timothy E; Gersbach, Charles A

    2017-06-01

    Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR-Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR-Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context. Using dCas9 KRAB repressor and dCas9 p300 activator constructs and lentiviral single guide RNA libraries to target DNase I hypersensitive sites surrounding a gene of interest, we carried out both loss- and gain-of-function screens to identify regulatory elements for the β-globin and HER2 loci in human cells. CERES readily identified known and previously unidentified regulatory elements, some of which were dependent on cell type or direction of perturbation. This technology allows the high-throughput functional annotation of putative regulatory elements in their native chromosomal context.

  7. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line.

    Science.gov (United States)

    Adey, Andrew; Burton, Joshua N; Kitzman, Jacob O; Hiatt, Joseph B; Lewis, Alexandra P; Martin, Beth K; Qiu, Ruolan; Lee, Choli; Shendure, Jay

    2013-08-08

    The HeLa cell line was established in 1951 from cervical cancer cells taken from a patient, Henrietta Lacks. This was the first successful attempt to immortalize human-derived cells in vitro. The robust growth and unrestricted distribution of HeLa cells resulted in its broad adoption--both intentionally and through widespread cross-contamination--and for the past 60 years it has served a role analogous to that of a model organism. The cumulative impact of the HeLa cell line on research is demonstrated by its occurrence in more than 74,000 PubMed abstracts (approximately 0.3%). The genomic architecture of HeLa remains largely unexplored beyond its karyotype, partly because like many cancers, its extensive aneuploidy renders such analyses challenging. We carried out haplotype-resolved whole-genome sequencing of the HeLa CCL-2 strain, examined point- and indel-mutation variations, mapped copy-number variations and loss of heterozygosity regions, and phased variants across full chromosome arms. We also investigated variation and copy-number profiles for HeLa S3 and eight additional strains. We find that HeLa is relatively stable in terms of point variation, with few new mutations accumulating after early passaging. Haplotype resolution facilitated reconstruction of an amplified, highly rearranged region of chromosome 8q24.21 at which integration of the human papilloma virus type 18 (HPV-18) genome occurred and that is likely to be the event that initiated tumorigenesis. We combined these maps with RNA-seq and ENCODE Project data sets to phase the HeLa epigenome. This revealed strong, haplotype-specific activation of the proto-oncogene MYC by the integrated HPV-18 genome approximately 500 kilobases upstream, and enabled global analyses of the relationship between gene dosage and expression. These data provide an extensively phased, high-quality reference genome for past and future experiments relying on HeLa, and demonstrate the value of haplotype resolution for

  8. Making Lists, Enlisting Scientists

    DEFF Research Database (Denmark)

    Jensen, Casper Bruun

    2011-01-01

    was the indicator conceptualised? How were notions of scientific knowledge and collaboration inscribed and challenged in the process? The analysis shows a two-sided process in which scientists become engaged in making lists but which is simultaneously a way for research policy to enlist scientists. In conclusion...

  9. Stories of Scientists.

    Science.gov (United States)

    Mascazine, John R.

    2001-01-01

    Presents three biographical sketches of scientists including John Wesley Powell (first to explore the geology of the Grand Canyon), Joseph von Fraunhofer (his work in optics led to the science of spectroscopy), and Gregor Mendel (of Mendelian genetics fame). Other scientists are mentioned along with sources for additional biographical information.…

  10. Young Scientist Wetenschapskalender 2018

    NARCIS (Netherlands)

    van Dalen-Oskam, K.H.; van Zundert, Joris J.; Koolen, Corina

    2017-01-01

    Bijdragen scheurkalender Young Scientist Wetenschapskalender 2018. Karina van Dalen-Oskam, Belangrijk woord: Wat is het belangrijkste woord in de Nederlandse taal? In: Young Scientist Wetenschapskalender 2018, 1 september Corina Koolen, Op naar het boekenbal: Hoe wordt je beroemd als schrijver? In:

  11. [Folates and fetal programming: role of epigenetics and epigenomics].

    Science.gov (United States)

    Guéant, Jean-Louis; Daval, Jean-Luc; Vert, Paul; Nicolas, Jean-Pierre

    2012-12-01

    Folates are needed for synthesis of methionine, the precursor of S-adenosyl methionine (SAM). They play therefore a key role in nutrition and epigenomics by fluxing monocarbons towards synthesis or methylation of DNA and RNA, and methylation of gene transregulators, respectively. The deficiency produces intrauterine growth retardation and birth dejects. Folate deficiency deregulates epigenomic mechanisms related to fetal programming through decreased cellular availability of SAM. Epigenetic mechanisms of folate deficiency are illustrated by inheritance of coat colour of agouti mice model and altered expression of Igf2/H19 imprinting genes. Dietary exposure to fumonisin FB1 acts synergistically with folate deficiency on alterations of heterochromatin assembly. Deficiency in folate and vitamin B12 produces impaired fatty acid oxidation in liver and heart through imbalanced methylation and acetylation of PGC1-alpha and decreased expression of SIRT1, and long-lasting cognitive disabilities through impaired hippocampal cell proliferation, differentiation and plasticity and atrophy of hippocampal CA1. Deciphering these mechanisms will help understand the discordances between experimental models and population studies on folate supplementation.

  12. ENCODE: A Sourcebook of Epigenomes and Chromatin Language

    Directory of Open Access Journals (Sweden)

    Maryam Yavartanoo

    2013-03-01

    Full Text Available Until recently, since the Human Genome Project, the general view has been that the majority of the human genome is composed of junk DNA and has little or no selective advantage to the organism. Now we know that this conclusion is an oversimplification. In April 2003, the National Human Genome Research Institute (NHGRI launched an international research consortium called Encyclopedia of DNA Elements (ENCODE to uncover non-coding functional elements in the human genome. The result of this project has identified a set of new DNA regulatory elements, based on novel relationships among chromatin accessibility, histone modifications, nucleosome positioning, DNA methylation, transcription, and the occupancy of sequence-specific factors. The project gives us new insights into the organization and regulation of the human genome and epigenome. Here, we sought to summarize particular aspects of the ENCODE project and highlight the features and data that have recently been released. At the end of this review, we have summarized a case study we conducted using the ENCODE epigenome data.

  13. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression.

    Science.gov (United States)

    Fiziev, Petko; Akdemir, Kadir C; Miller, John P; Keung, Emily Z; Samant, Neha S; Sharma, Sneha; Natale, Christopher A; Terranova, Christopher J; Maitituoheti, Mayinuer; Amin, Samirkumar B; Martinez-Ledesma, Emmanuel; Dhamdhere, Mayura; Axelrad, Jacob B; Shah, Amiksha; Cheng, Christine S; Mahadeshwar, Harshad; Seth, Sahil; Barton, Michelle C; Protopopov, Alexei; Tsai, Kenneth Y; Davies, Michael A; Garcia, Benjamin A; Amit, Ido; Chin, Lynda; Ernst, Jason; Rai, Kunal

    2017-04-25

    The extent and nature of epigenomic changes associated with melanoma progression is poorly understood. Through systematic epigenomic profiling of 35 epigenetic modifications and transcriptomic analysis, we define chromatin state changes associated with melanomagenesis by using a cell phenotypic model of non-tumorigenic and tumorigenic states. Computation of specific chromatin state transitions showed loss of histone acetylations and H3K4me2/3 on regulatory regions proximal to specific cancer-regulatory genes in important melanoma-driving cell signaling pathways. Importantly, such acetylation changes were also observed between benign nevi and malignant melanoma human tissues. Intriguingly, only a small fraction of chromatin state transitions correlated with expected changes in gene expression patterns. Restoration of acetylation levels on deacetylated loci by histone deacetylase (HDAC) inhibitors selectively blocked excessive proliferation in tumorigenic cells and human melanoma cells, suggesting functional roles of observed chromatin state transitions in driving hyperproliferative phenotype. Through these results, we define functionally relevant chromatin states associated with melanoma progression. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  14. Genomic and Epigenomic Insights into Nutrition and Brain Disorders

    Directory of Open Access Journals (Sweden)

    Margaret Joy Dauncey

    2013-03-01

    Full Text Available Considerable evidence links many neuropsychiatric, neurodevelopmental and neurodegenerative disorders with multiple complex interactions between genetics and environmental factors such as nutrition. Mental health problems, autism, eating disorders, Alzheimer’s disease, schizophrenia, Parkinson’s disease and brain tumours are related to individual variability in numerous protein-coding and non-coding regions of the genome. However, genotype does not necessarily determine neurological phenotype because the epigenome modulates gene expression in response to endogenous and exogenous regulators, throughout the life-cycle. Studies using both genome-wide analysis of multiple genes and comprehensive analysis of specific genes are providing new insights into genetic and epigenetic mechanisms underlying nutrition and neuroscience. This review provides a critical evaluation of the following related areas: (1 recent advances in genomic and epigenomic technologies, and their relevance to brain disorders; (2 the emerging role of non-coding RNAs as key regulators of transcription, epigenetic processes and gene silencing; (3 novel approaches to nutrition, epigenetics and neuroscience; (4 gene-environment interactions, especially in the serotonergic system, as a paradigm of the multiple signalling pathways affected in neuropsychiatric and neurological disorders. Current and future advances in these four areas should contribute significantly to the prevention, amelioration and treatment of multiple devastating brain disorders.

  15. The landscape for epigenetic/epigenomic biomedical resources

    Science.gov (United States)

    Shakya, Kabita; O'Connell, Mary J.; Ruskin, Heather J.

    2012-01-01

    Recent advances in molecular biology and computational power have seen the biomedical sector enter a new era, with corresponding development of Bioinformatics as a major discipline. Generation of enormous amounts of data has driven the need for more advanced storage solutions and shared access through a range of public repositories. The number of such biomedical resources is increasing constantly and mining these large and diverse data sets continues to present real challenges. This paper attempts a general overview of currently available resources, together with remarks on their data mining and analysis capabilities. Of interest here is the recent shift in focus from genetic to epigenetic/epigenomic research and the emergence and extension of resource provision to support this both at local and global scale. Biomedical text and numerical data mining are both considered, the first dealing with automated methods for analyzing research content and information extraction, and the second (broadly) with pattern recognition and prediction. Any summary and selection of resources is inherently limited, given the spectrum available, but the aim is to provide a guideline for the assessment and comparison of currently available provision, particularly as this relates to epigenetics/epigenomics. PMID:22874136

  16. Birth of prominent scientists

    Science.gov (United States)

    Reyes Gonzalez, Leonardo; Veloso, Francisco

    2018-01-01

    This paper analyzes the influence key scientists have in the development of a science and technology system. In particular, this work appraises the influence that star scientists have on the productivity and impact of young faculty, as well as on the likelihood that these young researchers become a leading personality in science. Our analysis confirms previous results that eminent scientist have a prime role in the development of a scientific system, especially within the context of an emerging economy like Mexico. In particular, in terms of productivity and visibility, this work shows that between 1984 and 2001 the elite group of physicists in Mexico (approximate 10% of all scientists working in physics and its related fields) published 42% of all publications, received 50% of all citations and bred 18% to 26% of new entrants. In addition our work shows that scientists that enter the system by the hand of a highly productive researcher increased their productivity on average by 28% and the ones that did it by the hand of a highly visible scientist received on average 141% more citations, vis-à-vis scholars that did not published their first manuscripts with an eminent scientist. Furthermore, scholars that enter the system by the hand of a highly productive researcher were on average 2.5 more likely to also become a star. PMID:29543855

  17. Birth of prominent scientists.

    Science.gov (United States)

    Reyes Gonzalez, Leonardo; González Brambila, Claudia N; Veloso, Francisco

    2018-01-01

    This paper analyzes the influence key scientists have in the development of a science and technology system. In particular, this work appraises the influence that star scientists have on the productivity and impact of young faculty, as well as on the likelihood that these young researchers become a leading personality in science. Our analysis confirms previous results that eminent scientist have a prime role in the development of a scientific system, especially within the context of an emerging economy like Mexico. In particular, in terms of productivity and visibility, this work shows that between 1984 and 2001 the elite group of physicists in Mexico (approximate 10% of all scientists working in physics and its related fields) published 42% of all publications, received 50% of all citations and bred 18% to 26% of new entrants. In addition our work shows that scientists that enter the system by the hand of a highly productive researcher increased their productivity on average by 28% and the ones that did it by the hand of a highly visible scientist received on average 141% more citations, vis-à-vis scholars that did not published their first manuscripts with an eminent scientist. Furthermore, scholars that enter the system by the hand of a highly productive researcher were on average 2.5 more likely to also become a star.

  18. Scientists and Human Rights

    Science.gov (United States)

    Makdisi, Yousef

    2012-02-01

    The American Physical Society has a long history of involvement in defense of human rights. The Committee on International Freedom of Scientists was formed in the mid seventies as a subcommittee within the Panel On Public Affairs ``to deal with matters of an international nature that endangers the abilities of scientists to function as scientists'' and by 1980 it was established as an independent committee. In this presentation I will describe some aspects of the early history and the impetus that led to such an advocacy, the methods employed then and how they evolved to the present CIFS responsibility ``for monitoring concerns regarding human rights for scientists throughout the world''. I will also describe the current approach and some sample cases the committee has pursued recently, the interaction with other human rights organizations, and touch upon some venues through which the community can engage to help in this noble cause.

  19. Scientists vs. the administration

    CERN Multimedia

    2004-01-01

    Article denouncing the supposed impartiality of signatories of a report released by the Union of Concerned Scientists (UCS), which accused the Bush administration of systemically suborning objective science to a political agenda (1 page).

  20. Scientists planning new internet

    CERN Multimedia

    Cookson, C

    2000-01-01

    British scientists are preparing to build the next generation internet - 'The Grid'. The government is expected to announce about 100 million pounds of funding for the project, to be done in collaboration with CERN (1/2 p).

  1. Scientists must speak

    National Research Council Canada - National Science Library

    Walters, D. Eric; Walters, Gale Climenson

    2011-01-01

    .... This can be a stressful experience for many. For scientists, the experience may be further complicated by the specialist nature of the data and the fact that most self-help books are aimed at business or social situations...

  2. The Celebrity Scientists

    OpenAIRE

    Fahy, Declan

    2010-01-01

    This collective case study examines how four contemporary British scientists and popular science writers, Stephen Hawking, Richard Dawkins, Susan Greenfield and James Lovelock, are portrayed in mass media as celebrities. It finds that the scientists’ private and public lives merge in their representations, their images commodified and marketed by the cultural industries, their mediated personae embodying abstract ideas of truth and reason. The celebrity scientists base their authority on thei...

  3. Grace hopper computer scientist

    CERN Document Server

    Wheeler, Jill C

    2017-01-01

    Women scientists have made key contributions to the pursuit of science and some of the most important discoveries of all time. In Grace Hopper, learn how the American computer scientist chose to pursue a career in science and revolutionized the way we program computers. Features include a timeline, a glossary, essential facts, references, websites, source notes, and an index. Aligned to Common Core Standards and correlated to state standards. Essential Library is an imprint of Abdo Publishing, a division of ABDO.

  4. The Epigenome and Transcriptional Dynamics of Fruit Ripening.

    Science.gov (United States)

    Giovannoni, James; Nguyen, Cuong; Ampofo, Betsy; Zhong, Silin; Fei, Zhangjun

    2017-04-28

    Fruit has evolved myriad forms that facilitate seed dispersal in varied environmental and ecological contexts. Because fleshy fruits become attractive and nutritious to seed-dispersing animals, the transition from unripe to ripe fruit represents a dramatic shift in survival strategy-from protecting unripe fruit against damaging animals to making it appealing to those same animals once ripened. For optimal fitness, ripening therefore must be tightly controlled and coordinated with seed development. Fruits, like many vegetative tissues of plants that contribute to human diets, are also subject to decay, which is enhanced as a consequence of the ripening transition. As such, ripening control has enormous relevance for both plant biology and food security. Here, we review the complex interactions of hormones and transcription factors during fleshy-fruit ripening, with an emphasis on the recent discovery that epigenome dynamics are a critical and early regulator of the cascade of molecular events that ultimately contribute to fruit maturation and ripening.

  5. Transgenerational epigenetic inheritance: adaptation through the germline epigenome?

    Science.gov (United States)

    Prokopuk, Lexie; Western, Patrick S; Stringer, Jessica M

    2015-08-01

    Epigenetic modifications direct the way DNA is packaged into the nucleus, making genes more or less accessible to transcriptional machinery and influencing genomic stability. Environmental factors have the potential to alter the epigenome, allowing genes that are silenced to be activated and vice versa. This ultimately influences disease susceptibility and health in an individual. Furthermore, altered chromatin states can be transmitted to subsequent generations, thus epigenetic modifications may provide evolutionary mechanisms that impact on adaptation to changed environments. However, the mechanisms involved in establishing and maintaining these epigenetic modifications during development remain unclear. This review discusses current evidence for transgenerational epigenetic inheritance, confounding issues associated with its study, and the biological relevance of altered epigenetic states for subsequent generations.

  6. MYC—Master Regulator of the Cancer Epigenome and Transcriptome

    Science.gov (United States)

    Poole, Candace J.; van Riggelen, Jan

    2017-01-01

    Overexpression of MYC is a hallmark of many human cancers. The MYC oncogene has long been thought to execute its neoplastic functions by acting as a classic transcription factor, deregulating the expression of a large number of specific target genes. However, MYC’s influence on many of these target genes is rather modest and there is little overlap between MYC regulated genes in different cell types, leaving many mechanistic questions unanswered. Recent advances in the field challenge the dogma further, revealing a role for MYC that extends beyond the traditional concept of a sequence-specific transcription factor. In this article, we review MYC’s function as a regulator of the cancer epigenome and transcriptome. We outline our current understanding of how MYC regulates chromatin structure in both a site-specific and genome-wide fashion, and highlight the implications for therapeutic strategies for cancers with high MYC expression. PMID:28505071

  7. ePIANNO: ePIgenomics ANNOtation tool.

    Directory of Open Access Journals (Sweden)

    Chia-Hsin Liu

    Full Text Available Recently, with the development of next generation sequencing (NGS, the combination of chromatin immunoprecipitation (ChIP and NGS, namely ChIP-seq, has become a powerful technique to capture potential genomic binding sites of regulatory factors, histone modifications and chromatin accessible regions. For most researchers, additional information including genomic variations on the TF binding site, allele frequency of variation between different populations, variation associated disease, and other neighbour TF binding sites are essential to generate a proper hypothesis or a meaningful conclusion. Many ChIP-seq datasets had been deposited on the public domain to help researchers make new discoveries. However, researches are often intimidated by the complexity of data structure and largeness of data volume. Such information would be more useful if they could be combined or downloaded with ChIP-seq data. To meet such demands, we built a webtool: ePIgenomic ANNOtation tool (ePIANNO, http://epianno.stat.sinica.edu.tw/index.html. ePIANNO is a web server that combines SNP information of populations (1000 Genomes Project and gene-disease association information of GWAS (NHGRI with ChIP-seq (hmChIP, ENCODE, and ROADMAP epigenomics data. ePIANNO has a user-friendly website interface allowing researchers to explore, navigate, and extract data quickly. We use two examples to demonstrate how users could use functions of ePIANNO webserver to explore useful information about TF related genomic variants. Users could use our query functions to search target regions, transcription factors, or annotations. ePIANNO may help users to generate hypothesis or explore potential biological functions for their studies.

  8. Epigenomics, gestational programming and risk of metabolic syndrome.

    Science.gov (United States)

    Desai, M; Jellyman, J K; Ross, M G

    2015-04-01

    Epigenetic mechanisms are emerging as mediators linking early environmental exposures during pregnancy with programmed changes in gene expression that alter offspring growth and development. There is irrefutable evidence from human and animal studies that nutrient and environmental agent exposures (for example, endocrine disruptors) during pregnancy may affect fetal/newborn development resulting in offspring obesity and obesity-associated metabolic abnormalities (metabolic syndrome). This concept of 'gestational programming' is associated with alterations to the epigenome (nongenomic) rather than changes in the DNA sequence (genomic). Epigenetic alterations induced by suboptimal maternal nutrition/endocrine factors include DNA methylation, histone modifications, chromatin remodeling and/or regulatory feedback by microRNAs, all of which have the ability to modulate gene expression and promote the metabolic syndrome phenotype. Recent studies have shown tissue-specific transcriptome patterns and phenotypes not only in the exposed individual, but also in subsequent progeny. Notably, the transmission of gestational programming effects to subsequent generations occurs in the absence of continued adverse environmental exposures, thus propagating the cycle of obesity and metabolic syndrome. This phenomenon may be attributed to an extrinsic process resulting from the maternal phenotype and the associated nutrient alterations occurring within each pregnancy. In addition, epigenetic inheritance may occur through somatic cells or through the germ line involving both maternal and paternal lineages. Since epigenetic gene modifications may be reversible, understanding how epigenetic mechanisms contribute to transgenerational transmission of obesity and metabolic dysfunction is crucial for the development of novel early detection and prevention strategies for programmed metabolic syndrome. In this review we discuss the evidence in human and animal studies for the role of

  9. Marketing for scientists

    CERN Document Server

    Kuchner, Marc J

    2012-01-01

    It's a tough time to be a scientist: universities are shutting science departments, funding organisations are facing flat budgets, and many newspapers have dropped their science sections altogether. But according to Marc Kuchner, this anti-science climate doesn't have to equal a career death knell - it just means scientists have to be savvier about promoting their work and themselves. In "Marketing for Scientists", he provides clear, detailed advice about how to land a good job, win funding, and shape the public debate. As an astrophysicist at NASA, Kuchner knows that "marketing" can seem like a superficial distraction, whether your daily work is searching for new planets or seeking a cure for cancer. In fact, he argues, it's a critical component of the modern scientific endeavour, not only advancing personal careers but also society's knowledge. Kuchner approaches marketing as a science in itself. He translates theories about human interaction and sense of self into methods for building relationships - one o...

  10. The scientist lady

    Indian Academy of Sciences (India)

    Lawrence

    many distinguished scientists among the list of students she trained. Her work conducted by her students showed that introduction of. Neera in the diet of tribal malnourished adolescent children and pregnant women, caused significant improvement in their overall health. She made her students (different batches) do this ...

  11. Ethics for life scientists

    NARCIS (Netherlands)

    Korthals, M.J.J.A.A.; Bogers, R.J.

    2004-01-01

    In this book we begin with two contributions on the ethical issues of working in organizations. A fruitful side effect of this start is that it gives a good insight into business ethics, a branch of applied ethics that until now is far ahead of ethics for life scientists. In the second part, ethics

  12. Reading about Real Scientists

    Science.gov (United States)

    Cummins, Sunday

    2015-01-01

    Although students do need hands-on experiences to master key skills in science, technology, and engineering, Cummins asserts, K-12 teachers should also help students understand key STEM concepts by reading, writing, and talking about the work of professional scientists and engineers. Cummins lists high-quality texts that help young people…

  13. Michael Polanyi, the Scientist

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 23; Issue 1. Comment: Michael Polanyi, the Scientist. John Polanyi. Article-in-a-Box Volume 23 Issue 1 January 2018 pp 15-19. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/023/01/0015-0019. Abstract ...

  14. Today's Authors, Tomorrow's Scientists

    Science.gov (United States)

    Porter, Diana

    2009-01-01

    Although not all teachers can invite scientists into classrooms on a regular basis, they can invite them into their students' worlds through literature. Here the author shares how she used the nonfiction selection, "Science to the Rescue" (Markle 1994), as an opportunity for students to investigate socially significant problems and empower them to…

  15. Vikram Sarabhai, the Scientist

    Indian Academy of Sciences (India)

    U R Rao, currently. Chairman of PRL. Governing Council, started his career as a cosmic ray scientist under Vikram Sarabhai and continued his research in USA as a prime experimenter on. Pioneer and Explorer. Series of Spacecrafts. On his return, he started the satellite program in India resulting in the launch of over 18 ...

  16. An Amateur Scientist

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 10. G. I. Taylor – An Amateur Scientist. Jaywant H Arakeri. Article-in-a-Box Volume 9 Issue 10 October 2004 pp 3-5. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/009/10/0003-0005 ...

  17. Developing Scientists' "Soft" Skills

    Science.gov (United States)

    Gordon, Wendy

    2014-02-01

    A great deal of professional advice directed at undergraduates, graduate students, postdoctoral fellows, and even early-career scientists focuses on technical skills necessary to succeed in a complex work environment in which problems transcend disciplinary boundaries. Collaborative research approaches are emphasized, as are cross-training and gaining nonacademic experiences [Moslemi et al., 2009].

  18. Michael Polanyi, the Scientist

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 23; Issue 1. Comment: Michael Polanyi, the Scientist. John Polanyi. Article-in-a-Box Volume 23 Issue 1 January 2018 pp 15-19. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/023/01/0015-0019. Abstract ...

  19. Epigenome-Wide Association Study of Tic Disorders.

    Science.gov (United States)

    Zilhão, Nuno R; Padmanabhuni, Shanmukha S; Pagliaroli, Luca; Barta, Csaba; Smit, Dirk J A; Cath, Danielle; Nivard, Michel G; Baselmans, Bart M L; van Dongen, Jenny; Paschou, Peristera; Boomsma, Dorret I

    2015-12-01

    Tic disorders are moderately heritable common psychiatric disorders that can be highly troubling, both in childhood and in adulthood. In this study, we report results obtained in the first epigenome-wide association study (EWAS) of tic disorders. The subjects are participants in surveys at the Netherlands Twin Register (NTR) and the NTR biobank project. Tic disorders were measured with a self-report version of the Yale Global Tic Severity Scale Abbreviated version (YGTSS-ABBR), included in the 8th wave NTR data collection (2008). DNA methylation data consisted of 411,169 autosomal methylation sites assessed by the Illumina Infinium HumanMethylation450 BeadChip Kit (HM450k array). Phenotype and DNA methylation data were available in 1,678 subjects (mean age = 41.5). No probes reached genome-wide significance (p tic disorders. The top significantly enriched gene ontology (GO) terms among higher ranking methylation sites included anatomical structure morphogenesis (GO:0009653, p = 4.6 × 10-(15)) developmental process (GO:0032502, p = 2.96 × 10(-12)), and cellular developmental process (GO:0048869, p = 1.96 × 10(-12)). Overall, these results provide a first insight into the epigenetic mechanisms of tic disorders. This first study assesses the role of DNA methylation in tic disorders, and it lays the foundations for future work aiming to unravel the biological mechanisms underlying the architecture of this disorder.

  20. Rapid and reversible epigenome editing by endogenous chromatin regulators.

    Science.gov (United States)

    Braun, Simon M G; Kirkland, Jacob G; Chory, Emma J; Husmann, Dylan; Calarco, Joseph P; Crabtree, Gerald R

    2017-09-15

    Understanding the causal link between epigenetic marks and gene regulation remains a central question in chromatin biology. To edit the epigenome we developed the FIRE-Cas9 system for rapid and reversible recruitment of endogenous chromatin regulators to specific genomic loci. We enhanced the dCas9-MS2 anchor for genome targeting with Fkbp/Frb dimerizing fusion proteins to allow chemical-induced proximity of a desired chromatin regulator. We find that mSWI/SNF (BAF) complex recruitment is sufficient to oppose Polycomb within minutes, leading to activation of bivalent gene transcription in mouse embryonic stem cells. Furthermore, Hp1/Suv39h1 heterochromatin complex recruitment to active promoters deposits H3K9me3 domains, resulting in gene silencing that can be reversed upon washout of the chemical dimerizer. This inducible recruitment strategy provides precise kinetic information to model epigenetic memory and plasticity. It is broadly applicable to mechanistic studies of chromatin in mammalian cells and is particularly suited to the analysis of endogenous multi-subunit chromatin regulator complexes.Understanding the link between epigenetic marks and gene regulation requires the development of new tools to directly manipulate chromatin. Here the authors demonstrate a Cas9-based system to recruit chromatin remodelers to loci of interest, allowing rapid, reversible manipulation of epigenetic states.

  1. Cross-species genomic and epigenomic landscape of retinoblastoma

    Science.gov (United States)

    Benavente, Claudia A.; McEvoy, Justina D.; Finkelstein, David; Wei, Lei; Kang, Guolian; Wang, Yong-Dong; Neale, Geoffrey; Ragsdale, Susan; Valentine, Virginia; Bahrami, Armita; Temirov, Jamshid; Pounds, Stanley; Zhang, Jinghui; Dyer, Michael A.

    2013-01-01

    Genetically engineered mouse models (GEMMs) of human cancer are important for advancing our understanding of tumor initiation and progression as well as for testing novel therapeutics. Retinoblastoma is a childhood cancer of the developing retina that initiates with biallelic inactivation of the RB1 gene. GEMMs faithfully recapitulate the histopathology, molecular, cellular, morphometric, neuroanatomical and neurochemical features of human retinoblastoma. In this study, we analyzed the genomic and epigenomic landscape of murine retinoblastoma and compared them to human retinoblastomas to gain insight into shared mechanisms of tumor progression across species. Similar to human retinoblastoma, mouse tumors have low rates of single nucleotide variations. However, mouse retinoblastomas have higher rates of aneuploidy and regional and focal copy number changes that vary depending on the genetic lesions that initiate tumorigenesis in the developing murine retina. Furthermore, the epigenetic landscape in mouse retinoblastoma was significantly different from human tumors and some pathways that are candidates for molecular targeted therapy for human retinoblastoma such as SYK or MCL1 are not deregulated in GEMMs. Taken together, these data suggest there are important differences between mouse and human retinoblastomas with respect to the mechanism of tumor progression and those differences can have significant implications for translational research to test the efficacy of novel therapies for this devastating childhood cancer. PMID:23765217

  2. Manipulating the epigenome for the treatment of urological malignancies.

    LENUS (Irish Health Repository)

    O'Rourke, Colm J

    2013-05-01

    Urological malignancies (cancers of the prostate, bladder, kidney and testes) account for 15% of all human cancers and more than 500,000 deaths worldwide each year. This group of malignancies is spread across multiple generations, affecting the young (testicular) through middle and old-age (kidney, prostate and bladder). Like most human cancers, urological cancers are characterized by widespread epigenetic insult, causing changes in DNA hypermethylation and histone modifications leading to silencing of tumor suppressor genes and genomic instability. The inherent stability yet dynamic plasticity of the epigenome lends itself well to therapeutic manipulation. Epigenetic changes are amongst the earliest lesions to occur during carcinogenesis and are essentially reversible (unlike mutations). For this reason, much attention has been placed over the past two decades on deriving pharmacological compounds that can specifically target and reverse such epi-mutations, either halting cancer on its developmental trajectory or reverting fully formed cancers to a more clinically manageable state. This review discusses DNA methyltransferase and histone deacetylase inhibitors that have been extensively studied in preclinical models and clinical trials for advanced and metastatic urological cancers.

  3. The epigenomics revolution in myelodysplasia: a clinico-pathological perspective.

    Science.gov (United States)

    Tan, Peter T; Wei, Andrew H

    2011-10-01

    Rapid advances in molecular technologies are continually re-shaping the way we view and understand the mechanisms driving oncogenesis. The last decade has witnessed unparalleled change in the biology and therapy of the myelodysplastic syndromes (MDS), a heterogeneous collection of clonal myeloid disorders characterised by ineffective haematopoiesis and susceptibility to acute leukaemia transformation. Pivotal studies demonstrating the positive effects of hypomethylating agents on clinical outcome have brought an 'epigenomics revolution' to this disease, emphasising the importance of epigenetic mechanisms to the underlying pathogenesis of MDS. One of the most important future challenges in the MDS field will be to determine whether epigenetic therapies can be made more 'targeted' through identification of biomarkers which define subsets of patients most likely to benefit from treatment. A wave of novel mutations have recently been reported in MDS and other myeloid disorders, several of which regulate endogenous methylation networks within cells (including TET2, DNMT3A, IDH and EZH2). The relevance of these lesions in being able to predict response to epigenetic modulators and their correlation with epigenetic signatures in MDS are beginning to emerge.

  4. Management Scientists Are Human

    OpenAIRE

    Geert Hofstede

    1994-01-01

    The culture of the national environment in which an organization operates affects the management process through the collective mental programming of its members, its managers, and the management scientists who offer their theories. Four dimensions of national culture differences have been found. Among other things, they affect the implicit models in people's minds of what the act of organizing means. Among the pioneers in management science around 1900, differences along these dimensions are...

  5. Ethics for life scientists

    OpenAIRE

    Korthals, M.J.J.A.A.; Bogers, R.J.

    2004-01-01

    In this book we begin with two contributions on the ethical issues of working in organizations. A fruitful side effect of this start is that it gives a good insight into business ethics, a branch of applied ethics that until now is far ahead of ethics for life scientists. In the second part, ethics of activities directly connected with doing scientific research are discussed, like experimenting with animals and human beings, publishing, patenting, getting funds and selecting one’s research th...

  6. Common Altered Epigenomic Domains in Cancer Cells: Characterization and Subtle Variations

    International Nuclear Information System (INIS)

    Tsai, Yi-Chien; Chiao, Chun-Hui; Chang, Ian Yi-Feng; Chen, Dow-Tien; Liu, Tze-Tze; Hua, Kate; Chang, Chuan-Hsiung; Hsu, Ming-Ta

    2011-01-01

    We have previously identified large megabase-sized hypomethylated zones in the genome of the breast cancer cell line MCF-7 using the TspRI-ExoIII technique. In this report, we used a more convenient high throughput method for mapping the hypomethylated zones in a number of human tumor genomes simultaneously. The method was validated by the bisulfite sequencing of 39 randomly chosen sites in a demethylated domain and by bisulfite genome-wide sequencing of the MCF-7 genome. This showed that the genomes of the various tumor cell lines, as well as some primary tumors, exhibit common hypomethylated domains. Interestingly, these hypomethylated domains are correlated with low CpG density distribution genome-wide, together with the histone H3K27Me3 landscape. Furthermore, they are inversely correlated with the H3K9Ac landscape and gene expression as measured in MCF-7 cells. Treatment with drugs resulted in en-bloc changes to the methylation domains. A close examination of the methylation domains found differences between non-invasive and invasive tumors with respect to tumorigenesis related genes. Taken together these results suggest that the human genome is organized in epigenomic domains that contain various different types of genes and imply that there are cis- and trans-regulators that control these domain-wide epigenetic changes and hence gene expression in the human genome. The hypomethylated domains are located in gene deserts that contain mainly tissue-specific genes and therefore we hypothesize that tumor cells keep these regions demethylated and silenced in order to save energy and resources and allow higher levels of cell proliferation and better survival (a thrifty tumor genome hypothesis)

  7. A Systemic Analysis of Transcriptomic and Epigenomic Data To Reveal Regulation Patterns for Complex Disease.

    Science.gov (United States)

    Xu, Chao; Zhang, Ji-Gang; Lin, Dongdong; Zhang, Lan; Shen, Hui; Deng, Hong-Wen

    2017-07-05

    Integrating diverse genomics data can provide a global view of the complex biological processes related to the human complex diseases. Although substantial efforts have been made to integrate different omics data, there are at least three challenges for multi-omics integration methods: (i) How to simultaneously consider the effects of various genomic factors, since these factors jointly influence the phenotypes; (ii) How to effectively incorporate the information from publicly accessible databases and omics datasets to fully capture the interactions among (epi)genomic factors from diverse omics data; and (iii) Until present, the combination of more than two omics datasets has been poorly explored. Current integration approaches are not sufficient to address all of these challenges together. We proposed a novel integrative analysis framework by incorporating sparse model, multivariate analysis, Gaussian graphical model, and network analysis to address these three challenges simultaneously. Based on this strategy, we performed a systemic analysis for glioblastoma multiforme (GBM) integrating genome-wide gene expression, DNA methylation, and miRNA expression data. We identified three regulatory modules of genomic factors associated with GBM survival time and revealed a global regulatory pattern for GBM by combining the three modules, with respect to the common regulatory factors. Our method can not only identify disease-associated dysregulated genomic factors from different omics, but more importantly, it can incorporate the information from publicly accessible databases and omics datasets to infer a comprehensive interaction map of all these dysregulated genomic factors. Our work represents an innovative approach to enhance our understanding of molecular genomic mechanisms underlying human complex diseases. Copyright © 2017 Xu et al.

  8. Ernest Rutherford: scientist supreme

    International Nuclear Information System (INIS)

    Campbell, J.

    1998-01-01

    One hundred years ago this month, Ernest Rutherford a talented young New Zealander who had just spent three years as a postgraduate student in Britain left for Canada, where he was to do the work that won him a Nobel prize. All three countries can justifiably claim this great scientist as their own. Ernest Rutherford is one of the most illustrious scientists that the world has ever seen. He achieved enduring international fame because of an incredibly productive life, during which he altered our view of nature on three separate occasions. Combining brilliantly conceived experiments with much hard work and special insight, he explained the perplexing problem of naturally occurring radioactivity, determined the structure of the atom, and was the world's first successful alchemist, changing nitrogen into oxygen. Rutherford received a Nobel prize for the first discovery, but the other two would have been equally worthy candidates, had they been discovered by someone else. Indeed, any one of his other secondary achievements many of which are now almost forgotten would have been enough to bring fame to a lesser scientist. For example, he invented an electrical method for detecting individual ionizing radiations, he dated the age of the Earth, and briefly held the world record for the distance over which wireless waves could be detected. He predicted the existence of neutrons, he oversaw the development of large-scale particle accelerators, and, during the First World War, he led the allied research into the detection of submarines. In this article the author describes the life and times of Ernest Rutherford. (UK)

  9. Soviet scientists speak out

    International Nuclear Information System (INIS)

    Holloway, D.

    1993-01-01

    In this article, Russian bomb designers answer the KGB's claim that espionage, not science, produced the Soviet bomb. Yuli Khariton and Yuri Smirnov wholly reject the argument that Soviet scientists can claim little credit for the first Soviet bomb. In a lecture delivered at the Kurchatov Institute, established in 1943 when Igor Kurchatov became the director of the Soviet nuclear weapons project, Khariton and Smironov point to the work done by Soviet nuclear physicists before 1941 and refute assertions that have been made in Western literature regarding the hydrogen bomb

  10. The influence of DNA sequence on epigenome-induced pathologies

    Directory of Open Access Journals (Sweden)

    Meagher Richard B

    2012-07-01

    Full Text Available Abstract Clear cause-and-effect relationships are commonly established between genotype and the inherited risk of acquiring human and plant diseases and aberrant phenotypes. By contrast, few such cause-and-effect relationships are established linking a chromatin structure (that is, the epitype with the transgenerational risk of acquiring a disease or abnormal phenotype. It is not entirely clear how epitypes are inherited from parent to offspring as populations evolve, even though epigenetics is proposed to be fundamental to evolution and the likelihood of acquiring many diseases. This article explores the hypothesis that, for transgenerationally inherited chromatin structures, “genotype predisposes epitype”, and that epitype functions as a modifier of gene expression within the classical central dogma of molecular biology. Evidence for the causal contribution of genotype to inherited epitypes and epigenetic risk comes primarily from two different kinds of studies discussed herein. The first and direct method of research proceeds by the examination of the transgenerational inheritance of epitype and the penetrance of phenotype among genetically related individuals. The second approach identifies epitypes that are duplicated (as DNA sequences are duplicated and evolutionarily conserved among repeated patterns in the DNA sequence. The body of this article summarizes particularly robust examples of these studies from humans, mice, Arabidopsis, and other organisms. The bulk of the data from both areas of research support the hypothesis that genotypes predispose the likelihood of displaying various epitypes, but for only a few classes of epitype. This analysis suggests that renewed efforts are needed in identifying polymorphic DNA sequences that determine variable nucleosome positioning and DNA methylation as the primary cause of inherited epigenome-induced pathologies. By contrast, there is very little evidence that DNA sequence directly

  11. Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens

    Science.gov (United States)

    2014-01-01

    Background Increasing evidence supports a role for altered gene expression in mediating the lasting effects of cocaine on the brain, and recent work has demonstrated the involvement of chromatin modifications in these alterations. However, all such studies to date have been restricted by their reliance on microarray technologies that have intrinsic limitations. Results We use next generation sequencing methods, RNA-seq and ChIP-seq for RNA polymerase II and several histone methylation marks, to obtain a more complete view of cocaine-induced changes in gene expression and associated adaptations in numerous modes of chromatin regulation in the mouse nucleus accumbens, a key brain reward region. We demonstrate an unexpectedly large number of pre-mRNA splicing alterations in response to repeated cocaine treatment. In addition, we identify combinations of chromatin changes, or signatures, that correlate with cocaine-dependent regulation of gene expression, including those involving pre-mRNA alternative splicing. Through bioinformatic prediction and biological validation, we identify one particular splicing factor, A2BP1(Rbfox1/Fox-1), which is enriched at genes that display certain chromatin signatures and contributes to drug-induced behavioral abnormalities. Together, this delineation of the cocaine-induced epigenome in the nucleus accumbens reveals several novel modes of regulation by which cocaine alters the brain. Conclusions We establish combinatorial chromatin and transcriptional profiles in mouse nucleus accumbens after repeated cocaine treatment. These results serve as an important resource for the field and provide a template for the analysis of other systems to reveal new transcriptional and epigenetic mechanisms of neuronal regulation. PMID:24758366

  12. The Epigenomics of Embryonic Pathway Signaling in Colorectal Cancer

    Directory of Open Access Journals (Sweden)

    Curt Balch

    2017-05-01

    Full Text Available Colorectal cancer (CRC is the second-leading cause of cancer death in developed countries. While early detection (e.g., colonoscopy generally yields excellent outcomes, metastatic and drug-resistant disease is uniformly fatal, and non-compliance for screening remains over 25%. Familial CRCs (10% of total cases primarily include mutations in the gene APC. Somatic disease is linked to several environmental several risk factors, including mutations in WNT, KRAS, and TGFβ. To reflect the genesis/progression of CRC, a series of five discrete stages, from normal colon mucosa to fully invasive carcinoma, each regulated by specific “gatekeeper” genes, remains well-accepted after 20 years. However, many CRC tumors do not possess those particular mutations, suggesting alternative mechanisms. More recently, embryo-like “cancer stem cells” have been proposed to undergo self-renewal and drive tumorigenesis (and possibly, metastasis, as governed by specific “epigenomic” alterations. Here, we review recent literature describing possible mechanisms that underlie these phenotypes, including cancer “stemness,” believed by many to associate with the epithelial-to-mesenchymal transition (EMT. We further propose that the maintenance of undifferentiated phenotypes, by the activity of distinct transcription factors, facilitates chromatin remodeling and phenotypic plasticity. With that regard, we support recent assertions that EMT is not an “either/or” event, but rather a continuous spectrum of mesenchymal vs. epithelial phenotypes (in various degrees of aberrant differentiation/undifferentiation. Finally, we discuss possible methods of pharmacologically targeting such aberrant epigenomes, with regard to their possible relevance toward halting, or even reversing, colorectal cancer progression.

  13. Endocrine Disrupters: the new players able to affect the epigenome.

    Directory of Open Access Journals (Sweden)

    Lavinia eCasati

    2015-06-01

    Full Text Available Epigenetics represents the way by which the environment is able to program the genome; there are three main levels of epigenetic control on genome: DNA methylation, post-translational histone modification and microRNA expression. The term Epigenetics has been widened by NIH to include both heritable changes in gene activity and expression but also stable, long-term alterations in the transcriptional potential of a cell that are not necessarily heritable. These changes might be produced mostly by the early life environment and might affect health influencing the susceptibility to develop diseases, from cancer to mental disorder, during the entire life span. The most studied environmental influences acting on epigenome are diet, infections, wasting, child care, smoking and environmental pollutants, in particular endocrine disrupters (EDs. These are environmental xenobiotics able to interfere with the normal development of the male and female reproductive systems of wildlife, of experimental animals and possibly of humans, disrupting the normal reproductive functions. Data from literature indicate that EDs can act at different levels of epigenetic control, in some cases transgenerationally, in particular when the exposure to these compounds occurs during the prenatal and earliest period of life. Some of the best characterized EDs will be considered in this review. Among the EDs, vinclozolin (VZ and methoxychlor (MXC promote epigenetic transgenerational effects. Polychlorinated biphenils (PCBs, the most widespread environmental EDs, affect histone post-translational modifications in a dimorphic way, possibly as the result of an alteration of gene expression of the enzymes involved in histone modification, as the demethylase Jarid1b, an enzyme also involved in regulating the interaction of androgens with their receptor.

  14. Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data.

    Directory of Open Access Journals (Sweden)

    Stephanie A Bien

    Full Text Available The evaluation of less frequent genetic variants and their effect on complex disease pose new challenges for genomic research. To investigate whether epigenetic data can be used to inform aggregate rare-variant association methods (RVAM, we assessed whether variants more significantly associated with colorectal cancer (CRC were preferentially located in non-coding regulatory regions, and whether enrichment was specific to colorectal tissues.Active regulatory elements (ARE were mapped using data from 127 tissues and cell-types from NIH Roadmap Epigenomics and Encyclopedia of DNA Elements (ENCODE projects. We investigated whether CRC association p-values were more significant for common variants inside versus outside AREs, or 2 inside colorectal (CR AREs versus AREs of other tissues and cell-types. We employed an integrative epigenomic RVAM for variants with allele frequency <1%. Gene sets were defined as ARE variants within 200 kilobases of a transcription start site (TSS using either CR ARE or ARE from non-digestive tissues. CRC-set association p-values were used to evaluate enrichment of less frequent variant associations in CR ARE versus non-digestive ARE.ARE from 126/127 tissues and cell-types were significantly enriched for stronger CRC-variant associations. Strongest enrichment was observed for digestive tissues and immune cell types. CR-specific ARE were also enriched for stronger CRC-variant associations compared to ARE combined across non-digestive tissues (p-value = 9.6 × 10-4. Additionally, we found enrichment of stronger CRC association p-values for rare variant sets of CR ARE compared to non-digestive ARE (p-value = 0.029.Integrative epigenomic RVAM may enable discovery of less frequent variants associated with CRC, and ARE of digestive and immune tissues are most informative. Although distance-based aggregation of less frequent variants in CR ARE surrounding TSS showed modest enrichment, future association studies would likely

  15. Scientists--Geeks and Nerds?

    Science.gov (United States)

    McDuffie, Thomas E., Jr.

    2001-01-01

    Investigates teachers' impressions of stereotypes of scientists and science. Uses the Draw a Scientist Test (DAST) for nonverbal assessment and makes recommendations for strategies to build more realistic and positive images. (Contains 12 references.) (YDS)

  16. [The happy scientist].

    Science.gov (United States)

    Tijdink, Joeri K; Vergouwen, Anton C M; Smulders, Yvo M

    2012-01-01

    The H-index is a frequently used scale to rank scientists on their scientific output. Whether subjective feeling of happiness is influenced by the level of the H-index on scientists has never been investigated. To investigate the relation between the level of the H index as a measure of scientific success and feelings of unhappiness among Dutch professors. Descriptive; national online questionnaire. All medical professors working at the Dutch university medical centres were invited to participate in an online questionnaire. Pressure to publish was measured by a questionnaire developed for this purpose and signs of burnout were measured on the Utrecht Burnout Scale. The area of emotional exhaustion on this scale was used to measure feelings of unhappiness. Every professor was asked for his or her H-index as an outcome measure. A total of 437 professors completed the questionnaire. Those in the highest tertile of the H index had significantly lower scores for emotional exhaustion (p emotional exhaustion. Professors with children living at home had a 25% higher score on emotional exhaustion than those who did not (p emotional exhaustion: a lower H index is associated with higher scores on emotional exhaustion while a high H index is associated with lower scores.

  17. WFIRST CGI Adjutant Scientist

    Science.gov (United States)

    Kasdin, N.

    One of the most exciting developments in exoplanet science is the inclusion of a coronagraph instrument on WFIRST. After more than 20 years of research and development on coronagraphy and wavefront control, the technology is ready for a demonstration in space and to be used for revolutionary science. Good progress has already been made at JPL and partner institutions on the coronagraph technology and instrument design and test. The next five years as we enter Phase A will be critical for raising the TRL of the coronagraph to the needed level for flight and for converging on a design that is robust, low risk, and meets the science requirements. In addition, there is growing excitement over the possibility of rendezvousing an occulter with WFIRST/AFTA as a separate mission; this would both demonstrate that important technology and potentially dramatically enhance the science reach, introducing the possibility of imaging Earth-like planets in the habitable zone of nearby stars. In this proposal I will be applying for the Coronagraph Adjutant Scientist (CAS) position. I bring to the position the background and skills needed to be an effective liaison between the project office, the instrument team, and the Science Investigation Team (SIT). My background in systems engineering before coming to Princeton (I was Chief Systems Engineer for the Gravity Probe-B mission) and my 15 years of working closely with NASA on both coronagraph and occulter technology make me well-suited to the role. I have been a lead coronagraph scientist for the WFIRST mission from the beginning, including as a member of the SDT. Together with JPL and NASA HQ, I helped organize the process for selecting the coronagraphs for the CGI, one of which, the shaped pupil, has been developed in my lab. All of the key algorithms for wavefront control (including EFC and Stroke Minimization) were originally developed by students or post-docs in my lab at Princeton. I am thus in a unique position to work with

  18. Another Kind of Scientist Activism

    Science.gov (United States)

    Marino, Lori

    2009-01-01

    In a well-cited 1996 editorial in "Science," "The Activist Scientist," Jaleh Daie calls for scientists to take an assertive role in educating politicians and the public about the importance of government support for research. She writes that most scientists are reluctant to become involved in political lobbying for a variety of reasons--time…

  19. Developmental Potential among Creative Scientists

    Science.gov (United States)

    Culross, Rita R.

    2008-01-01

    The world of creative scientists is dramatically different in the 21st century than it was during previous centuries. Whether biologists, chemists, physicists, engineers, mathematicians, or computer scientists, the livelihood of research scientists is dependent on their abilities of creative expression. The view of a solitary researcher who…

  20. How Scientists Can Become Entrepreneurs.

    Science.gov (United States)

    Thon, Jonathan N; Karlsson, Sven

    2017-05-01

    Translating basic research discoveries through entrepreneurship must be scientist driven and institutionally supported to be successful (not the other way around). Here, we describe why scientists should engage in entrepreneurship, where institutional support for scientist-founders falls short, and how these challenges can be overcome. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. How Scientists Can Become Entrepreneurs

    OpenAIRE

    Thon, Jonathan N.; Karlsson, Sven

    2017-01-01

    Translating basic research discoveries through entrepreneurship must be scientist driven and institutionally supported to be successful (not the other way around). Here, we describe why scientists should engage in entrepreneurship, where institutional support for scientist-founders falls short, and how these challenges can be overcome.

  2. Scientists in the public sphere: Interactions of scientists and journalists in Brazil.

    Science.gov (United States)

    Massarani, Luisa; Peters, Hans P

    2016-06-07

    In order to map scientists' views on media channels and explore their experiences interacting with journalists, the authors conducted a survey of about 1,000 Brazilian scientists. Results indicate that scientists have clear and high expectations about how journalists should act in reporting scientific information in the media, but such expectations, in their opinion, do not always seem to be met. Nonetheless, the results show that surveyed scientists rate their relation with the media positively: 67% say that having their research covered by media has a positive impact on their colleagues. One quarter of the respondents expressed that talking to the media can facilitate acquisition of more funds for research. Moreover, 38% of the total respondents believe that writing about an interesting topic for release on media channels can also facilitate research publication in a scientific journal. However, 15% of the respondents outright agree that research reported in the media beforehand can threaten acceptance for publication by a scientific journal. We hope that these results can foster some initiatives for improving awareness of the two cultures, scientists and journalists; increasing the access of journalists to Brazilian scientific endeavors; stimulating scientists to communicate with the public via social networks.

  3. Voices of Romanian scientists

    CERN Multimedia

    Stefania Pandolfi

    2016-01-01

    As Romania has now become a Member State of CERN, Romanian scientists share their thoughts about this new era of partnership for their community.   Members of ATLAS from Romanian institutes at CERN (from left to right): Dan Ciubotaru, Michele Renda, Bogdan Blidaru, Alexandra Tudorache, Marina Rotaru, Ana Dumitriu, Valentina Tudorache, Adam Jinaru, Calin Alexa. On 17 July 2016, Romania became the twenty-second Member State of CERN, 25 years after the first cooperation agreement with the country was signed. “CERN and Romania already have a long history of strong collaboration”, says Emmanuel Tsesmelis, head of Relations with Associate Members and Non-Member States. “We very much look forward to strengthening this collaboration as Romania becomes CERN’s twenty-second Member State, which promises the development of mutual interests in scientific research, related technologies and education,” he affirms. Romania&...

  4. Civil Liberties of Scientists.

    Science.gov (United States)

    1949-08-19

    On Decemrber 30, 1947 the AAAS Council passed a resolution instructing the President of the Association to appoint a Special Committee on Civil Liberties for Scientists. Maurice B. Visscher was named chairman, and with Philip Bard, Robert E. Cushman, Richard L. MVeier, and James R. Ncwmen as members, and Walter Gellhorn as consultant, the Committee completed its investigations and submitted a 77-page report of findings and recommendations in December 1948. The full text was referred to the Council, which voted by an overwhelming majority to publicize the findings, and it is planned ultimately to make the complete report available at cost to those who want access to it. Announcement will be made in Science when Maurice B. Visscher and E. C. Stakman have concluded editorial revisions and the report is ready for distribution. Meanwhile, by vote of the Executive Committee at its meeting July 7, the conclusions and recommendations are published herewith.

  5. Python for scientists

    CERN Document Server

    Stewart, John M

    2017-01-01

    Scientific Python is a significant public domain alternative to expensive proprietary software packages. This book teaches from scratch everything the working scientist needs to know using copious, downloadable, useful and adaptable code snippets. Readers will discover how easy it is to implement and test non-trivial mathematical algorithms and will be guided through the many freely available add-on modules. A range of examples, relevant to many different fields, illustrate the language's capabilities. The author also shows how to use pre-existing legacy code (usually in Fortran77) within the Python environment, thus avoiding the need to master the original code. In this new edition, several chapters have been re-written to reflect the IPython notebook style. With an extended index, an entirely new chapter discussing SymPy and a substantial increase in the number of code snippets, researchers and research students will be able to quickly acquire all the skills needed for using Python effectively.

  6. Forgotten women the scientists

    CERN Document Server

    Tsjeng, Zing

    2018-01-01

    The women who shaped and were erased from our history. The Forgotten Women series will uncover the lost histories of the influential women who have refused over hundreds of years to accept the hand they've been dealt and, as a result, have formed, shaped and changed the course of our futures. The Scientists celebrates 48* unsung scientific heroines whose hugely important, yet broadly unacknowledged or incorrectly attributed, discoveries have transformed our understanding of the scientific world. Mary Anning, the amateur paleontologist whose fossil findings changed scientific thinking about prehistoric life Emmy Noether, dubbed "The Mighty Mathematician You've Never Heard Of" Ynés Mexía, the Mexican-American botanist who discovered over 500 new plant species Wangari Maathai, who started an environmental and ecological revolution in Kenya Margaret Sanger, the maverick nurse who paved the way for the legalization of contraception Chapters including Earth & Universe; Biology & N...

  7. ECNS '99 - Young scientists forum

    DEFF Research Database (Denmark)

    Ceretti, M.; Janssen, S.; McMorrow, D.F.

    2000-01-01

    The Young Scientists Forum is a new venture for ECNS and follows the established tradition of an active participation by young scientists in these conferences. At ECNS '99 the Young Scientists Forum brought together 30 young scientists from 13 European countries. In four working groups......, they discussed emerging scientific trends in their areas of expertise and the instrumentation required to meet the scientific challenges. The outcome was presented in the Young Scientists Panel on the final day of ECNS '99. This paper is a summary of the four working group reports prepared by the Group Conveners...

  8. Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

    Directory of Open Access Journals (Sweden)

    David A. Orlando

    2014-11-01

    Full Text Available Epigenomic profiling by chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq is a prevailing methodology used to investigate chromatin-based regulation in biological systems such as human disease, but the lack of an empirical methodology to enable normalization among experiments has limited the precision and usefulness of this technique. Here, we describe a method called ChIP with reference exogenous genome (ChIP-Rx that allows one to perform genome-wide quantitative comparisons of histone modification status across cell populations using defined quantities of a reference epigenome. ChIP-Rx enables the discovery and quantification of dynamic epigenomic profiles across mammalian cells that would otherwise remain hidden using traditional normalization methods. We demonstrate the utility of this method for measuring epigenomic changes following chemical perturbations and show how reference normalization of ChIP-seq experiments enables the discovery of disease-relevant changes in histone modification occupancy.

  9. Dynamic histone H3 epigenome marking during the intraerythrocytic cycle of Plasmodium falciparum

    DEFF Research Database (Denmark)

    Salcedo-Amaya, Adriana M; van Driel, Marc A; Alako, Blaise T

    2009-01-01

    Epigenome profiling has led to the paradigm that promoters of active genes are decorated with H3K4me3 and H3K9ac marks. To explore the epigenome of Plasmodium falciparum asexual stages, we performed MS analysis of histone modifications and found a general preponderance of H3/H4 acetylation and H3K4......me3. ChIP-on-chip profiling of H3, H3K4me3, H3K9me3, and H3K9ac from asynchronous parasites revealed an extensively euchromatic epigenome with heterochromatin restricted to variant surface antigen gene families (VSA) and a number of genes hitherto unlinked to VSA. Remarkably, the vast majority...... of the genome shows an unexpected pattern of enrichment of H3K4me3 and H3K9ac. Analysis of synchronized parasites revealed significant developmental stage specificity of the epigenome. In rings, H3K4me3 and H3K9ac are homogenous across the genes marking active and inactive genes equally, whereas in schizonts...

  10. Comparative epigenomics: an emerging field with breakthrough potential to understand evolution of epigenetic regulation

    Directory of Open Access Journals (Sweden)

    Janine E. Deakin

    2014-12-01

    Full Text Available Epigenetic mechanisms regulate gene expression, thereby mediating the interaction between environment, genotype and phenotype. Changes to epigenetic regulation of genes may be heritable, permitting rapid adaptation of a species to environmental cues. However, most of the current understanding of epigenetic gene regulation has been gained from studies of mice and humans, with only a limited understanding of the conservation of epigenetic mechanisms across divergent taxa. The relative ease at which genome sequence data is now obtained and the advancements made in epigenomics techniques for non-model species provides a basis for carrying out comparative epigenomic studies across a wider range of species, making it possible to start unraveling the evolution of epigenetic mechanisms. We review the current knowledge of epigenetic mechanisms obtained from studying model organisms, give an example of how comparative epigenomics using non-model species is helping to trace the evolutionary history of X chromosome inactivation in mammals and explore the opportunities to study comparative epigenomics in biological systems displaying adaptation between species, such as the immune system and sex determination.

  11. Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity.

    Science.gov (United States)

    Clark, Stephen J; Lee, Heather J; Smallwood, Sébastien A; Kelsey, Gavin; Reik, Wolf

    2016-04-18

    Emerging single-cell epigenomic methods are being developed with the exciting potential to transform our knowledge of gene regulation. Here we review available techniques and future possibilities, arguing that the full potential of single-cell epigenetic studies will be realized through parallel profiling of genomic, transcriptional, and epigenetic information.

  12. CRISPR Epigenome Editing of AKAP150 in DRG Neurons Abolishes Degenerative IVD-Induced Neuronal Activation.

    Science.gov (United States)

    Stover, Joshua D; Farhang, Niloofar; Berrett, Kristofer C; Gertz, Jason; Lawrence, Brandon; Bowles, Robby D

    2017-09-06

    Back pain is a major contributor to disability and has significant socioeconomic impacts worldwide. The degenerative intervertebral disc (IVD) has been hypothesized to contribute to back pain, but a better understanding of the interactions between the degenerative IVD and nociceptive neurons innervating the disc and treatment strategies that directly target these interactions is needed to improve our understanding and treatment of back pain. We investigated degenerative IVD-induced changes to dorsal root ganglion (DRG) neuron activity and utilized CRISPR epigenome editing as a neuromodulation strategy. By exposing DRG neurons to degenerative IVD-conditioned media under both normal and pathological IVD pH levels, we demonstrate that degenerative IVDs trigger interleukin (IL)-6-induced increases in neuron activity to thermal stimuli, which is directly mediated by AKAP and enhanced by acidic pH. Utilizing this novel information on AKAP-mediated increases in nociceptive neuron activity, we developed lentiviral CRISPR epigenome editing vectors that modulate endogenous expression of AKAP150 by targeted promoter histone methylation. When delivered to DRG neurons, these epigenome-modifying vectors abolished degenerative IVD-induced DRG-elevated neuron activity while preserving non-pathologic neuron activity. This work elucidates the potential for CRISPR epigenome editing as a targeted gene-based pain neuromodulation strategy. Copyright © 2017 The American Society of Gene and Cell Therapy. Published by Elsevier Inc. All rights reserved.

  13. PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition.

    Science.gov (United States)

    Durham, Timothy J; Libbrecht, Maxwell W; Howbert, J Jeffry; Bilmes, Jeff; Noble, William Stafford

    2018-04-11

    The Encyclopedia of DNA Elements (ENCODE) and the Roadmap Epigenomics Project seek to characterize the epigenome in diverse cell types using assays that identify, for example, genomic regions with modified histones or accessible chromatin. These efforts have produced thousands of datasets but cannot possibly measure each epigenomic factor in all cell types. To address this, we present a method, PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition (PREDICTD), to computationally impute missing experiments. PREDICTD leverages an elegant model called "tensor decomposition" to impute many experiments simultaneously. Compared with the current state-of-the-art method, ChromImpute, PREDICTD produces lower overall mean squared error, and combining the two methods yields further improvement. We show that PREDICTD data captures enhancer activity at noncoding human accelerated regions. PREDICTD provides reference imputed data and open-source software for investigating new cell types, and demonstrates the utility of tensor decomposition and cloud computing, both promising technologies for bioinformatics.

  14. Phytochemical Antioxidants Modulate Mammalian Cellular Epigenome: Implications in Health and Disease

    Science.gov (United States)

    Malireddy, Smitha; Kotha, Sainath R.; Secor, Jordan D.; Gurney, Travis O.; Abbott, Jamie L.; Maulik, Gautam; Maddipati, Krishna R.

    2012-01-01

    In living systems, the mechanisms of inheritance involving gene expression are operated by (i) the traditional model of genetics where the deoxyribonucleic acid (DNA) transcription and messenger ribonucleic acid stability are influenced by the DNA sequences and any aberrations in the primary DNA sequences and (ii) the epigenetic (above genetics) model in which the gene expression is regulated by mechanisms other than the changes in DNA sequences. The widely studied epigenetic alterations include DNA methylation, covalent modification of chromatin structure, state of histone acetylation, and involvement of microribonucleic acids. Significance: Currently, the role of cellular epigenome in health and disease is rapidly emerging. Several factors are known to modulate the epigenome-regulated gene expression that is crucial in several pathophysiological states and diseases in animals and humans. Phytochemicals have occupied prominent roles in human diet and nutrition as protective antioxidants in prevention/protection against several disorders and diseases in humans. Recent Advances: However, it is beginning to surface that the phytochemical phenolic antioxidants such as polyphenols, flavonoids, and nonflavonoid phenols function as potent modulators of the mammalian epigenome-regulated gene expression through regulation of DNA methylation, histone acetylation, and histone deacetylation in experimental models. Critical Issues and Future Directions: The antioxidant or pro-oxidant actions and their involvement in the epigenome regulation by the phytochemical phenolic antioxidants should be at least established in the cellular models under normal and pathophysiological states. The current review discusses the mechanisms of modulation of the mammalian cellular epigenome by the phytochemical phenolic antioxidants with implications in human diseases. Antioxid. Redox Signal. 17, 327–339. PMID:22404530

  15. Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes.

    Science.gov (United States)

    Mirouze, Marie; Vitte, Clémentine

    2014-06-01

    In the past decade, plant biologists and breeders have developed a growing interest in the field of epigenetics, which is defined as the study of heritable changes in gene expression that cannot be explained by changes in the DNA sequence. Epigenetic marks can be responsive to the environment, and evolve faster than genetic changes. Therefore, epigenetic diversity may represent an unexplored resource of natural variation that could be used in plant breeding programmes. On the other hand, crop genomes are largely populated with transposable elements (TEs) that are efficiently targeted by epigenetic marks, and part of the epigenetic diversity observed might be explained by TE polymorphisms. Characterizing the degree to which TEs influence epigenetic variation in crops is therefore a major goal to better use epigenetic variation. To date, epigenetic analyses have been mainly focused on the model plant Arabidopsis thaliana, and have provided clues on epigenome features, components that silence pathways, and effects of silencing impairment. But to what extent can Arabidopsis be used as a model for the epigenomics of crops? In this review, we discuss the similarities and differences between the epigenomes of Arabidopsis and crops. We explore the relationship between TEs and epigenomes, focusing on TE silencing control and escape, and the impact of TE mobility on epigenomic variation. Finally, we provide insights into challenges to tackle, and future directions to take in the route towards using epigenetic diversity in plant breeding programmes. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  16. Genome and Epigenome Editing in Mechanistic Studies of Human Aging and Aging-Related Disease.

    Science.gov (United States)

    Lau, Cia-Hin; Suh, Yousin

    2017-01-01

    The recent advent of genome and epigenome editing technologies has provided a new paradigm in which the landscape of the human genome and epigenome can be precisely manipulated in their native context. Genome and epigenome editing technologies can be applied to many aspects of aging research and offer the potential to develop novel therapeutics against age-related diseases. Here, we discuss the latest technological advances in the CRISPR-based genome and epigenome editing toolbox, and provide insight into how these synthetic biology tools could facilitate aging research by establishing in vitro cell and in vivo animal models to dissect genetic and epigenetic mechanisms underlying aging and age-related diseases. We discuss recent developments in the field with the aims to precisely modulate gene expression and dynamic epigenetic landscapes in a spatial and temporal manner in cellular and animal models, by complementing the CRISPR-based editing capability with conditional genetic manipulation tools including chemically inducible expression systems, optogenetics, logic gate genetic circuits, tissue-specific promoters, and the serotype-specific adeno-associated virus. We also discuss how the combined use of genome and epigenome editing tools permits investigators to uncover novel molecular pathways involved in the pathophysiology and etiology conferred by risk variants associated with aging and aging-related disease. A better understanding of the genetic and epigenetic regulatory mechanisms underlying human aging and age-related disease will significantly contribute to the developments of new therapeutic interventions for extending health span and life span, ultimately improving the quality of life in the elderly populations. © 2016 S. Karger AG, Basel.

  17. Epigenome-wide DNA methylation study of IgE concentration in relation to self-reported allergies.

    Science.gov (United States)

    Ek, Weronica E; Ahsan, Muhammad; Rask-Andersen, Mathias; Liang, Liming; Moffatt, Miriam F; Gyllensten, Ulf; Johansson, Åsa

    2017-04-01

    Epigenetic mechanisms are critical for normal immune development and epigenetic alterations might therefore be possible contributors to immune diseases. To investigate if DNA methylation in whole blood is associated with total and allergen-specific IgE levels. We performed an epigenome-wide association study to investigate the association between DNA methylation and IgE level, allergen-specific IgE and self-reported immune diseases and allergies in 728 individuals. We identified and replicated 15 CpG sites associated with IgE, mapping to biologically relevant genes, including ACOT7, ILR5A, KCNH2, PRG2 and EPX. A total of 331 loci were associated with allergen-specific IgE, but none of these CpG sites were associated with self-reported allergies and immune diseases. This study shows that IgE levels are associated with DNA methylation levels at numerous CpG sites, which might provide new leads for investigating the links between IgE and allergic inflammation.

  18. Seven scientists advise

    International Nuclear Information System (INIS)

    1959-01-01

    The Scientific Advisory Committee of the International Atomic Energy Agency held its second series of meetings in Vienna on 4-5 June 1959. The members of the Committee are seven distinguished scientists from different countries: Dr. H.J. Bhabha (India), Sir John Cockcroft (UK), Professor V.S. Emelyanov (USSR), Dr. B. Goldschmidt (France), Dr. B. Gross (Brazil), Dr. W.B. Lewis (Canada) and Professor I.I. Rabi (USA). The function of the Committee is to provide the Director General and through him the Board of Governors with scientific and technical advice on questions relating to the Agency's activities. Subjects for consideration by the Committee can be submitted by the Director General either on his own behalf or on behalf of the Board. At its recent session, the Committee considered several aspects of the Agency's scientific programme, including the proposed conferences, symposia and seminars for 1960, scientific and technical publications, and the research contracts which had been or were to be awarded by the Agency. The programme of conferences for the current year had been approved earlier by the Board of Governors on the recommendation of the Committee. A provisional list of 17 conferences, symposia and seminars for 1960 was examined by the Committee and recommendations were made to the Director General. The Committee also examined the Agency's policy on the award of contracts for research work and studies. An important subject before the Committee was the principles and regulations for the application of Agency safeguards. Another subject considered by the Committee was the possibility of a project for an exchange of knowledge on controlled thermonuclear fusion. The Committee also examined a proposal for the determination of the world-wide distribution of hydrogen and oxygen isotopes in water. Exact information on the distribution of hydrogen and oxygen isotopes in rain, in rivers, in ground water and in oceans would be important for areas with limited water

  19. The Genomic Epigenomic, and Quality-of-Life Charteristics of Long-Term Survivors of Ovarian Cancer

    Science.gov (United States)

    2017-10-01

    AWARD NUMBER: W81XWH-16-2-0038 TITLE: The Genomic Epigenomic, and Quality -of-Life Charteristics of Long-Term Survivors of Ovarian Cancer...2017 Survivors of Ovarian Cancer 5a. CONTRACT NUMBER 4. TITLE AND SUBTITLE The Genomic Epigenomic, and Quality -of-Life Charteristics of Long-Term...therapy, and understanding the biology of their tumors, is significant both from a patient survival and quality of life (QOL) standpoint. The

  20. Probing scientists' beliefs: how open-minded are modern scientists?

    Science.gov (United States)

    Coll, Richard K.; Taylor, Neil

    2004-06-01

    Just how open-minded are modern scientists? In this paper we examine this question for the science faculty from New Zealand and UK universities. The Exeter questionnaire used by Preece and Baxter (2000) to examine superstitious beliefs of high school students and preservice science teachers was used as a basis for a series of in-depth interviews of scientists across a variety of disciplines. The interviews sought to understand the basis on which scientists form beliefs and how they judge evidence for various propositions, including those from the Exeter questionnaire and other contentious beliefs introduced during discourse. The scientists are dismissive of traditional superstitions like bad luck associated with black cats and inauspicious numbers such as 13, seeing such beliefs as socially grounded. There is a strong socio-cultural aspect to other beliefs and personal experiences, and strongly held personal beliefs are influential, resulting in the scientists keeping an open mind about contentious beliefs like alien life and the existence of ghosts. Testimony of others including media reports are deemed unreliable unless provided by credible witnesses such as 'educated people' or 'experts', or if they coincide with the scientists' personal beliefs. These scientists see a need for potential theoretical explanations for beliefs and are generally dismissive of empirical evidence without underlying explanations.

  1. Frontier Scientists use Modern Media

    Science.gov (United States)

    O'connell, E. A.

    2013-12-01

    Engaging Americans and the international community in the excitement and value of Alaskan Arctic discovery is the goal of Frontier Scientists. With a changing climate, resources of polar regions are being eyed by many nations. Frontier Scientists brings the stories of field scientists in the Far North to the public. With a website, an app, short videos, and social media channels; FS is a model for making connections between the public and field scientists. FS will demonstrate how academia, web content, online communities, evaluation and marketing are brought together in a 21st century multi-media platform, how scientists can maintain their integrity while engaging in outreach, and how new forms of media such as short videos can entertain as well as inspire.

  2. Genome Sequencing Technologies and Nursing: What Are the Roles of Nurses and Nurse Scientists?

    Science.gov (United States)

    Taylor, Jacquelyn Y; Wright, Michelle L; Hickey, Kathleen T; Housman, David E

    Advances in DNA sequencing technology have resulted in an abundance of personalized data with challenging clinical utility and meaning for clinicians. This wealth of data has potential to dramatically impact the quality of healthcare. Nurses are at the focal point in educating patients regarding relevant healthcare needs; therefore, an understanding of sequencing technology and utilizing these data are critical. The objective of this study was to explicate the role of nurses and nurse scientists as integral members of healthcare teams in improving understanding of DNA sequencing data and translational genomics for patients. A history of the nurse role in newborn screening is used as an exemplar. This study serves as an exemplar on how genome sequencing has been utilized in nursing science and incorporates linkages of other omics approaches used by nurses that are included in this special issue. This special issue showcased nurse scientists conducting multi-omic research from various methods, including targeted candidate genes, pharmacogenomics, proteomics, epigenomics, and the microbiome. From this vantage point, we provide an overview of the roles of nurse scientists in genome sequencing research and provide recommendations for the best utilization of nurses and nurse scientists related to genome sequencing.

  3. Dr.seq2: A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data.

    Directory of Open Access Journals (Sweden)

    Chengchen Zhao

    Full Text Available An increasing number of single cell transcriptome and epigenome technologies, including single cell ATAC-seq (scATAC-seq, have been recently developed as powerful tools to analyze the features of many individual cells simultaneously. However, the methods and software were designed for one certain data type and only for single cell transcriptome data. A systematic approach for epigenome data and multiple types of transcriptome data is needed to control data quality and to perform cell-to-cell heterogeneity analysis on these ultra-high-dimensional transcriptome and epigenome datasets. Here we developed Dr.seq2, a Quality Control (QC and analysis pipeline for multiple types of single cell transcriptome and epigenome data, including scATAC-seq and Drop-ChIP data. Application of this pipeline provides four groups of QC measurements and different analyses, including cell heterogeneity analysis. Dr.seq2 produced reliable results on published single cell transcriptome and epigenome datasets. Overall, Dr.seq2 is a systematic and comprehensive QC and analysis pipeline designed for parallel single cell transcriptome and epigenome data. Dr.seq2 is freely available at: http://www.tongji.edu.cn/~zhanglab/drseq2/ and https://github.com/ChengchenZhao/DrSeq2.

  4. Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host

    Science.gov (United States)

    Timp, Winston; Feinberg, Andrew P.

    2015-01-01

    Although at the genetic level cancer is caused by diverse mutations, epigenetic modifications are characteristic of all cancers, from apparently normal precursor tissue to advanced metastatic disease, and these epigenetic modifications drive tumour cell heterogeneity. We propose a unifying model of cancer in which epigenetic dysregulation allows rapid selection for tumour cell survival at the expense of the host. Mechanisms involve both genetic mutations and epigenetic modifications that disrupt the function of genes that regulate the epigenome itself. Several exciting recent discoveries also point to a genome-scale disruption of the epigenome that involves large blocks of DNA hypomethylation, mutations of epigenetic modifier genes and alterations of heterochromatin in cancer (including large organized chromatin lysine modifications (LOCKs) and lamin-associated domains (LADs)), all of which increase epigenetic and gene expression plasticity. Our model suggests a new approach to cancer diagnosis and therapy that focuses on epigenetic dysregulation and has great potential for risk detection and chemoprevention. PMID:23760024

  5. The openness of pluripotent epigenome - Defining the genomic integrity of stemness for regenerative medicine

    Directory of Open Access Journals (Sweden)

    Xuejun H Parsons

    2014-02-01

    Full Text Available This article is an editorial, and it doesn't include an abstract. Full text of this article is available in HTML and PDF.Cite this article as: Parsons XH. The openness of pluripotent epigenome - Defining the genomic Integrity of stemness for regenerative medicine. Int J Cancer Ther Oncol 2014; 2(1:020114.DOI: http://dx.doi.org/10.14319/ijcto.0201.14

  6. Epigenome engineering in cancer: fairytale or a realistic path to the clinic?

    Directory of Open Access Journals (Sweden)

    Fahimeh eFalahi

    2015-02-01

    Full Text Available Epigenetic modifications such as histone post-transcriptional modifications and DNA methylation organize the DNA in the nucleus of eukaryotic cells and are critical for the spatio-temporal regulation of gene expression. These epigenetic modifications are reversible and precisely regulated by epigenetic enzymes. In addition to genetic mutations, epigenetic modifications are highly disrupted in cancer relative to normal tissues. Many epigenetic alterations (epi-mutations are associated with aberrations in the expression and/or activity of epigenetic enzymes. Thus, epigenetic regulators have emerged as prime targets for cancer therapy. Currently, several inhibitors of epigenetic enzymes (epi-drugs have been approved for use in the clinic to treat cancer patients with hematological malignancies. However, one potential disadvantage of epi-drugs is their lack of locus-selective specificity, which may result in the over-expression of undesirable parts of the genome. The emerging and rapidly growing field of epigenome engineering has opened new grounds for improving epigenetic therapy in view of reducing the genome-wide off-target effects of the treatment. In the current review, we will first describe the language of epigenetic modifications and their involvement in cancer. Next, we will overview the current strategies for engineering of artificial DNA binding domains in order to manipulate and ultimately normalize the aberrant landscape of the cancer epigenome (epigenome engineering. Lastly, the potential clinical applications of these emerging genome-engineering approaches will be discussed.

  7. Chapter 4 genomics, transcriptomics, and epigenomics in traumatic brain injury research.

    Science.gov (United States)

    Puccio, Ava M; Alexander, Sheila

    2015-01-01

    The long-term effects and significant impact of the full spectrum of traumatic brain injury (TBI) has received increased attention in recent years. Despite increased research efforts, there has been little movement toward improving outcomes for the survivors of TBI. TBI is a heterogeneous condition with a complex biological response, and significant variability in human recovery contributes to the difficulty in identifying therapeutics that improve outcomes. Personalized medicine, identifying the best course of treatment for a given individual based on individual characteristics, has great potential to improve recovery for TBI survivors. The advances in medical genetics and genomics over the past 20 years have increased our understanding of many biological processes. A substantial amount of research has focused on the genomic, transcriptomic, and epigenomic profiles in many health and disease states, including recovery from TBI. The focus of this review chapter is to describe the current state of the science in genomic, transcriptomic, and epigenomic research in the TBI population. There have been some advancements toward understanding the genomic, transcriptomic, and epigenomic processes in humans, but much of this work remains at the preclinical stage. This current evidence does improve our understanding of TBI recovery, but also serves as an excellent platform upon which to build further study toward improved outcomes for this population.

  8. Distinct Epigenomic Landscapes of Pluripotent and Lineage-committed Human Cells

    Science.gov (United States)

    Hawkins, R. David; Hon, Gary C.; Lee, Leonard K.; Ngo, QueMinh; Lister, Ryan; Pelizzola, Mattia; Edsall, Lee E.; Kuan, Samantha; Luu, Ying; Klugman, Sarit; Antosiewicz-Bourget, Jessica; Ye, Zhen; Espinoza, Celso; Agarwahl, Saurabh; Shen, Li; Ruotti, Victor; Wang, Wei; Stewart, Ron; Thomson, James A.; Ecker, Joseph R.; Ren, Bing

    2010-01-01

    SUMMARY Human embryonic stem cells (hESCs) share an identical genome with lineage-committed cells, yet possess the remarkable properties of self-renewal and pluripotency. The diverse cellular properties in different cells have been attributed to their distinct epigenomes, but how much epigenomes differ remains unclear. Here, we report that epigenomic landscapes in hESC and lineage committed cells are drastically different. By comparing the chromatin modification profiles and DNA methylomes in hESCs and primary fibroblasts, we find that nearly one-third of the genome differs in chromatin structure. Most changes arise from dramatic redistributions of repressive H3K9me3 and H3K27me3 marks, which form blocks that significantly expand in fibroblasts. A large number of potential regulatory sequences also exhibit a high degree of dynamics in chromatin modifications and DNA methylation. Additionally, we observe novel, context-dependent relationships between DNA methylation and chromatin modifications. Our results provide new insights into epigenetic mechanisms underlying properties of pluripotency and cell-fate commitment. PMID:20452322

  9. Prader-Willi Syndrome: The Disease that Opened up Epigenomic-Based Preemptive Medicine

    Directory of Open Access Journals (Sweden)

    Takeo Kubota

    2016-03-01

    Full Text Available Prader-Willi syndrome (PWS is a congenital neurodevelopmental disorder caused by loss of function of paternally expressed genes on chromosome 15 due to paternal deletion of 15q11–q13, maternal uniparental disomy for chromosome 15, or an imprinting mutation. We previously developed a DNA methylation-based PCR assay to identify each of these three genetic causes of PWS. The assay enables straightforward and rapid diagnosis during infancy and therefore allows early intervention such as nutritional management, physical therapy, or growth hormone treatment to prevent PWS patients from complications such as obesity and type 2 diabetes. It is known that various environmental factors induce epigenomic changes during the perinatal period, which increase the risk of adult diseases such as type 2 diabetes and intellectual disabilities. Therefore, a similar preemptive approach as used in PWS would also be applicable to acquired disorders and would make use of environmentally-introduced “epigenomic signatures” to aid development of early intervention strategies that take advantage of “epigenomic reversibility”.

  10. Transitioning from genotypes to epigenotypes: why the time has come for medulloblastoma epigenomics.

    Science.gov (United States)

    Batora, N V; Sturm, D; Jones, D T W; Kool, M; Pfister, S M; Northcott, P A

    2014-04-04

    Recent advances in genomic technologies have allowed for tremendous progress in our understanding of the biology underlying medulloblastoma, a malignant childhood brain tumor. Consensus molecular subgroups have been put forth by the pediatric neuro-oncology community and next-generation genomic studies have led to an improved description of driver genes and pathways somatically altered in these subgroups. In contrast to the impressive pace at which advances have been made at the level of the medulloblastoma genome, comparable studies of the epigenome have lagged behind. Complementary data yielded from genomic sequencing and copy number profiling have verified frequent targeting of chromatin modifiers in medulloblastoma, highly suggestive of prominent epigenetic deregulation in the disease. Past studies of DNA methylation-dependent gene silencing and microRNA expression analyses further support the concept of medulloblastoma as an epigenetic disease. In this Review, we aim to summarize the key findings of past reports pertaining to medulloblastoma epigenetics as well as recent and ongoing genomic efforts linking somatic alterations of the genome with inferred deregulation of the epigenome. In addition, we predict what is on the horizon for medulloblastoma epigenetics and how aberrant changes in the medulloblastoma epigenome might serve as an attractive target for future therapies. Copyright © 2013 IBRO. Published by Elsevier Ltd. All rights reserved.

  11. SCIENCE, SCIENTISTS, AND POLICY ADVOCACY

    Science.gov (United States)

    Effectively resolving the typical ecological policy issue requires providing an array of scientific information to decision-makers. In my experience, the ability of scientists (and scientific information) to inform constructively ecological policy deliberations has been diminishe...

  12. Refugee scientists under the spotlight

    Science.gov (United States)

    Extance, Andy

    2017-07-01

    Thousands of people are forced to flee war-torn regions every year, but the struggles of scientists who have to leave their homeland often goes under the radar. Andy Extance reports on initiatives to help

  13. Scientists' views about communication objectives.

    Science.gov (United States)

    Besley, John C; Dudo, Anthony; Yuan, Shupei

    2017-08-01

    This study looks at how United States-based academic scientists from five professional scientific societies think about eight different communication objectives. The degree to which scientists say they would prioritize these objectives in the context of face-to-face public engagement is statistically predicted using the scientists' attitudes, normative beliefs, and efficacy beliefs, as well as demographics and past communication activity, training, and past thinking about the objectives. The data allow for questions about the degree to which such variables consistently predict views about objectives. The research is placed in the context of assessing factors that communication trainers might seek to reshape if they wanted get scientists to consider choosing specific communication objectives.

  14. Young Scientist in Classroom

    Science.gov (United States)

    Doran, Rosa

    very powerful tool that allows educators to address a diversity of topics ranging from ICT tools to the Exploration of our Universe. Instead of using traditional methods to teach about certain subjects for instance: stellar spectra, extra-solar planets or the classification of galaxies, they can use these powerful tools. Among other advantages a clear benefit of such tool is that teachers can use telescopes during regular classroom hours, provided they choose one located in the opposite part of the planet, where it is night time. Participants will also have the opportunity to use one of the radio antennas devoted for education from the EUHOU Consortium (European Hands-on Universe). A map of the arms of our galaxy will be built during the training session. Image Processing - After acquiring the images participants will be introduced to Salsa J, an image processing software that allows educators to explore the potential of astronomical images. The first example will be a simple measurement task: measuring craters on the Moon. Further exploration will guide them from luminosity studies to the construction of colour images, from making movies exhibiting the circular motion of the Sun to Jupiter Moons dance around the planet. e-learning repositories - In the ICT age it is very important that educators have support and know where to find meaningful and curriculum adapted resources for the construction of modern lessons. Some repositories will be presented in this session. Examples of such repositories are: Discover the Cosmos and EUHOU or a congregator of such repositories with quite advanced possibilities to support the work of teachers, the Open Discovery Space portal. This type of sessions are being successfully implemented by the Galileo Teacher Training Program team in Portugal under the scope of the EC funded GO-LAB project. This is a project devoted to demonstrate innovative ways to involve teachers and students in e-Science through the use of virtual labs, that

  15. Professional Ethics for Climate Scientists

    Science.gov (United States)

    Peacock, K.; Mann, M. E.

    2014-12-01

    Several authors have warned that climate scientists sometimes exhibit a tendency to "err on the side of least drama" in reporting the risks associated with fossil fuel emissions. Scientists are often reluctant to comment on the implications of their work for public policy, despite the fact that because of their expertise they may be among those best placed to make recommendations about such matters as mitigation and preparedness. Scientists often have little or no training in ethics or philosophy, and consequently they may feel that they lack clear guidelines for balancing the imperative to avoid error against the need to speak out when it may be ethically required to do so. This dilemma becomes acute in cases such as abrupt ice sheet collapse where it is easier to identify a risk than to assess its probability. We will argue that long-established codes of ethics in the learned professions such as medicine and engineering offer a model that can guide research scientists in cases like this, and we suggest that ethical training could be regularly incorporated into graduate curricula in fields such as climate science and geology. We recognize that there are disanalogies between professional and scientific ethics, the most important of which is that codes of ethics are typically written into the laws that govern licensed professions such as engineering. Presently, no one can legally compel a research scientist to be ethical, although legal precedent may evolve such that scientists are increasingly expected to communicate their knowledge of risks. We will show that the principles of professional ethics can be readily adapted to define an ethical code that could be voluntarily adopted by scientists who seek clearer guidelines in an era of rapid climate change.

  16. Do scientists trace hot topics?

    Science.gov (United States)

    Wei, Tian; Li, Menghui; Wu, Chensheng; Yan, Xiao-Yong; Fan, Ying; di, Zengru; Wu, Jinshan

    2013-07-01

    Do scientists follow hot topics in their scientific investigations? In this paper, by performing analysis to papers published in the American Physical Society (APS) Physical Review journals, it is found that papers are more likely to be attracted by hot fields, where the hotness of a field is measured by the number of papers belonging to the field. This indicates that scientists generally do follow hot topics. However, there are qualitative differences among scientists from various countries, among research works regarding different number of authors, different number of affiliations and different number of references. These observations could be valuable for policy makers when deciding research funding and also for individual researchers when searching for scientific projects.

  17. The Local-Cosmopolitan Scientist

    Directory of Open Access Journals (Sweden)

    Barney G. Glaser, Ph.D., Hon. Ph.D.

    2011-12-01

    Full Text Available In contrast to previous discussions in the literature treating cosmopolitan and local as two distinct groups of scientists, this paperi demonstrates the notion of cosmopolitan and local as a dual orientation of highly motivated scientists. This dual orientation is derived from institutional motivation, which is a determinant of both high quality basic research and accomplishment of non-research organizational activities. The dual orientation arises in a context of similarity of the institutional goal of science with the goal of the organization; the distinction between groups of locals and cosmopolitans derives from a conflict between two goals.

  18. How scientists develop competence in visual communication

    Science.gov (United States)

    Ostergren, Marilyn

    Visuals (maps, charts, diagrams and illustrations) are an important tool for communication in most scientific disciplines, which means that scientists benefit from having strong visual communication skills. This dissertation examines the nature of competence in visual communication and the means by which scientists acquire this competence. This examination takes the form of an extensive multi-disciplinary integrative literature review and a series of interviews with graduate-level science students. The results are presented as a conceptual framework that lays out the components of competence in visual communication, including the communicative goals of science visuals, the characteristics of effective visuals, the skills and knowledge needed to create effective visuals and the learning experiences that promote the acquisition of these forms of skill and knowledge. This conceptual framework can be used to inform pedagogy and thus help graduate students achieve a higher level of competency in this area; it can also be used to identify aspects of acquiring competence in visual communication that need further study.

  19. JBS Haldane: an uncommon scientist

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 96; Issue 5. J. B. S. Haldane: an uncommon scientist. M. S. SWAMINATHAN. HALDANE AT 125 Volume 96 Issue 5 November 2017 pp 731-732. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/jgen/096/05/0731-0732. Keywords.

  20. Comprehensive mathematics for computer scientists

    CERN Document Server

    Mazzola, Guerino; Weissmann, Jody

    2005-01-01

    This two-volume textbook Comprehensive Mathematics for the Working Computer Scientist is a self-contained comprehensive presentation of mathematics including sets, numbers, graphs, algebra, logic, grammars, machines, linear geometry, calculus, ODEs, and special themes such as neural networks, Fourier theory, wavelets, numerical.

  1. Wilhelm Ostwald–The Scientist

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 17; Issue 5. Wilhelm Ostwald –The Scientist. Pallavi Bhattacharyya. Article-in-a-Box Volume 17 Issue 5 May 2012 pp 428-433. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/017/05/0428-0433 ...

  2. Epigenomic alterations and gene expression profiles in respiratory epithelia exposed to cigarette smoke condensate.

    Science.gov (United States)

    Liu, F; Killian, J K; Yang, M; Walker, R L; Hong, J A; Zhang, M; Davis, S; Zhang, Y; Hussain, M; Xi, S; Rao, M; Meltzer, P A; Schrump, D S

    2010-06-24

    Limited information is available regarding epigenomic events mediating initiation and progression of tobacco-induced lung cancers. In this study, we established an in vitro system to examine epigenomic effects of cigarette smoke in respiratory epithelia. Normal human small airway epithelial cells and cdk-4/hTERT-immortalized human bronchial epithelial cells (HBEC) were cultured in normal media with or without cigarette smoke condensate (CSC) for up to 9 months under potentially relevant exposure conditions. Western blot analysis showed that CSC mediated dose- and time-dependent diminution of H4K16Ac and H4K20Me3, while increasing relative levels of H3K27Me3; these histone alterations coincided with decreased DNA methyltransferase 1 (DNMT1) and increased DNMT3b expression. Pyrosequencing and quantitative RT-PCR experiments revealed time-dependent hypomethylation of D4Z4, NBL2, and LINE-1 repetitive DNA sequences; up-regulation of H19, IGF2, MAGE-A1, and MAGE-A3; activation of Wnt signaling; and hypermethylation of tumor suppressor genes such as RASSF1A and RAR-beta, which are frequently silenced in human lung cancers. Array-based DNA methylation profiling identified additional novel DNA methylation targets in soft-agar clones derived from CSC-exposed HBEC; a CSC gene expression signature was also identified in these cells. Progressive genomic hypomethylation and locoregional DNA hypermethylation induced by CSC coincided with a dramatic increase in soft-agar clonogenicity. Collectively, these data indicate that cigarette smoke induces 'cancer-associated' epigenomic alterations in cultured respiratory epithelia. This in vitro model may prove useful for delineating early epigenetic mechanisms regulating gene expression during pulmonary carcinogenesis.

  3. Modulation of the Genome and Epigenome of Individuals Susceptible to Autism by Environmental Risk Factors

    Directory of Open Access Journals (Sweden)

    Costas Koufaris

    2015-04-01

    Full Text Available Diverse environmental factors have been implicated with the development of autism spectrum disorders (ASD. Genetic factors also underlie the differential vulnerability to environmental risk factors of susceptible individuals. Currently the way in which environmental risk factors interact with genetic factors to increase the incidence of ASD is not well understood. A greater understanding of the metabolic, cellular, and biochemical events involved in gene x environment interactions in ASD would have important implications for the prevention and possible treatment of the disorder. In this review we discuss various established and more alternative processes through which environmental factors implicated in ASD can modulate the genome and epigenome of genetically-susceptible individuals.

  4. Epigenome-wide association study of cognitive functioning in middle-aged monozygotic twins

    DEFF Research Database (Denmark)

    Starnawska, Anna; Tan, Qihua; McGue, Matt

    2017-01-01

    As the world's population ages, the age-related cognitive decline presents a great challenge to world's healthcare systems. One of the molecular mechanisms implicated in cognitive ageing is DNA methylation, an epigenetic modification known to be a key player in memory formation, maintenance......, and synaptic plasticity. Using the twin design we performed an epigenome-wide association study (EWAS) in a population of 486 middle-aged monozygotic twins (mean age at follow-up 65.9, SD = 6.1) and correlated their blood DNA methylation to their level (cross-sectional analysis) and change in cognitive...

  5. The Impact of External Factors on the Epigenome: In Utero and over Lifetime

    Science.gov (United States)

    Toraño, Estela G.; García, María G.; Fernández-Morera, Juan Luis; Niño-García, Pilar; Fernández, Agustín F.

    2016-01-01

    Epigenetic marks change during fetal development, adult life, and aging. Some changes play an important role in the establishment and regulation of gene programs, but others seem to occur without any apparent physiological role. An important future challenge in the field of epigenetics will be to describe how the environment affects both of these types of epigenetic change and to learn if interaction between them can determine healthy and disease phenotypes during lifetime. Here we discuss how chemical and physical environmental stressors, diet, life habits, and pharmacological treatments can affect the epigenome during lifetime and the possible impact of these epigenetic changes on pathophysiological processes. PMID:27294112

  6. Ovarian cancer plasticity and epigenomics in the acquisition of a stem-like phenotype

    Directory of Open Access Journals (Sweden)

    Berry Nicholas B

    2008-11-01

    Full Text Available Abstract Aggressive epithelial ovarian cancer (EOC is genetically and epigenetically distinct from normal ovarian surface epithelial cells (OSE and early neoplasia. Co-expression of epithelial and mesenchymal markers in EOC suggests an involvement of epithelial-mesenchymal transition (EMT in cancer initiation and progression. This phenomenon is often associated with acquisition of a stem cell-like phenotype and chemoresistance that correlate with the specific gene expression patterns accompanying transformation, revealing a plasticity of the ovarian cancer cell genome during disease progression. Differential gene expressions between normal and transformed cells reflect the varying mechanisms of regulation including genetic changes like rearrangements within the genome, as well as epigenetic changes such as global genomic hypomethylation with localized promoter CpG island hypermethylation. The similarity of gene expression between ovarian cancer cells and the stem-like ovarian cancer initiating cells (OCIC are surprisingly also correlated with epigenetic mechanisms of gene regulation in normal stem cells. Both normal and cancer stem cells maintain genetic flexibility by co-placement of activating and/or repressive epigenetic modifications on histone H3. The co-occupancy of such opposing histone marks is believed to maintain gene flexibility and such bivalent histones have been described as being poised for transcriptional activation or epigenetic silencing. The involvement of both-microRNA (miRNA mediated epigenetic regulation, as well as epigenetic-induced changes in miRNA expression further highlight an additional complexity in cancer stem cell epigenomics. Recent advances in array-based whole-genome/epigenome analyses will continue to further unravel the genomes and epigenomes of cancer and cancer stem cells. In order to illuminate phenotypic signatures that delineate ovarian cancer from their associated cancer stem cells, a priority must lie

  7. A first glance on the epigenome of Capra hircus

    Directory of Open Access Journals (Sweden)

    Stefano Frattini

    2015-07-01

    Full Text Available DNA methylation and microRNAs (miRNA are two important forms of epigenetic modifications that play an important role in gene regulation in animals. Methylation at the carbon 5 position of cytosine residues is a fundamental layer of cellular differentiation through the control of transcriptional potential. MiRNA are small noncoding RNA molecules that regulate gene expression. Complete DNA methylomes for several organisms are now available; at the present, methylome of the domestic goat is unexplored. There is also still limited knowledge about miRNAs expression profiles in small ruminant species. Therefore, to contribute information on epigenetic modification in Capra hircus, we analysed the methylome and the miRNA population of three tissues (hypothalamus, pituitary and ovary from 3 adult Saanen goats. We used Methylated DNA binding domain sequencing with enrichment of methylated DNA fragments and next generation sequencing. We produced least 23 million reads per sample, which were aligned to the goat reference genome. Further analyses were performed to identify peaks corresponding to hyper-methylated regions. We sequenced miRNAs expressed in the three tissues with Illumina high-throughput sequencing. Reads were mapped on the Capra hircus reference genome and both known and novel miRNAs, and miRNA target sites were identified using information collected in miRBase and using specific bioinformatic tools. This study produced a comprehensive miRNA profile related to the biology of goat. Furthermore, this is the first work dealing with methylome in Capra hircus: our preliminary results could provide new information for a deeper comprehension of epigenetic mechanisms of this species.

  8. Poll of radiation health scientists

    International Nuclear Information System (INIS)

    Cohen, B.L.

    1986-01-01

    A sampling of 210 university-employed radiation health scientists randomly selected from the membership lists of the Health Physics Society and the Radiation Research Society was polled in a secret ballot. The results support the positions that the public's fear of radiation is substantially greater than realistic, that TV, newspapers and magazines substantially exaggerate the dangers of radiation, that the amount of money now being spent on radiation protection is sufficient, and that the openness and honesty of U.S. government agencies about dangers of radiation were below average before 1972 but have been above average since then. Respondents give very high credibility ratings to BEIR, UNSCEAR, ICRP, and NCRP and to the individual scientists associated with their reports, and very low credibility ratings to those who have disputed them

  9. Mathematics for engineers and scientists

    CERN Document Server

    Jeffrey, Alan

    2004-01-01

    Although designed as a textbook with problem sets in each chapter and selected answers at the end of the book, Mathematics for Engineers and Scientists, Sixth Edition serves equally well as a supplemental text and for self-study. The author strongly encourages readers to make use of computer algebra software, to experiment with it, and to learn more about mathematical functions and the operations that it can perform.

  10. Research Integrity of Individual Scientist

    Science.gov (United States)

    Haklak, Rockbill

    We are discussing about many aspects of research integrity of individual scientist, who faces the globalization of research ethics in the traditional culture and custom of Japan. Topics are scientific misconduct (fabrication, falsification, and plagiarism) in writing paper and presenting research results. Managements of research material, research record, grant money, authorship, and conflict of interest are also analyzed and discussed. Finally, we make 5 recommendations to improve research integrity in Japan.

  11. Thermodynamics for scientists and engineers

    International Nuclear Information System (INIS)

    Lim, Gyeong Hui

    2011-02-01

    This book deals with thermodynamics for scientists and engineers. It consists of 11 chapters, which are concept and background of thermodynamics, the first law of thermodynamics, the second law of thermodynamics and entropy, mathematics related thermodynamics, properties of thermodynamics on pure material, equilibrium, stability of thermodynamics, the basic of compound, phase equilibrium of compound, excess gibbs energy model of compound and activity coefficient model and chemical equilibrium. It has four appendixes on properties of pure materials and thermal mass.

  12. Political action committee for scientists

    Science.gov (United States)

    Richman, Barbara T.

    Spurred by budget proposals that could severely reduce science funding (Eos, March 24, March 3, February 10), seven scientists currently serving as Congressional Science or State Department Fellows recently founded a political action committee (PAC) for scientists. The Science and Technology Political Action Committee (SCITEC-PAC) aims to make scientists more politically aware and better informed about potential legislative actions that affect research. It will also serve to ‘establish a political presence’ with respect to science, said Donald Stein, SCITEC-PAC's chairman.The organization is not a lobbying group, explained Stein, professor of neurology and psychology at Clark University and the University of Massachusetts Medical Center. ‘Lobbyists seek to influence officials by presenting information to them,’ he said, ‘while a PAC tries to influence the outcome of elections through campaign contributions of money, time, and effort in behalf of candidates that share similar goals and aspirations.’ In other words, the PAC will be a vehicle for promoting candidates for federal office who advocate strong support for scientific research and training. In addition, the PAC will develop and study science policy and budget issues and will attempt to stimulate government and private sector interest in these issues.

  13. Epigenome-wide profiling of DNA methylation in paired samples of adipose tissue and blood.

    Science.gov (United States)

    Huang, Yen-Tsung; Chu, Su; Loucks, Eric B; Lin, Chien-Ling; Eaton, Charles B; Buka, Stephen L; Kelsey, Karl T

    2016-03-03

    Many epigenetic association studies have attempted to identify DNA methylation markers in blood that are able to mirror those in target tissues. Although some have suggested potential utility of surrogate epigenetic markers in blood, few studies have collected data to directly compare DNA methylation across tissues from the same individuals. Here, epigenomic data were collected from adipose tissue and blood in 143 subjects using Illumina HumanMethylation450 BeadChip array. The top axis of epigenome-wide variation differentiates adipose tissue from blood, which is confirmed internally using cross-validation and externally with independent data from the two tissues. We identified 1,285 discordant genes and 1,961 concordant genes between blood and adipose tissue. RNA expression data of the two classes of genes show consistent patterns with those observed in DNA methylation. The discordant genes are enriched in biological functions related to immune response, leukocyte activation or differentiation, and blood coagulation. We distinguish the CpG-specific correlation from the within-subject correlation and emphasize that the magnitude of within-subject correlation does not guarantee the utility of surrogate epigenetic markers. The study reinforces the critical role of DNA methylation in regulating gene expression and cellular phenotypes across tissues, and highlights the caveats of using methylation markers in blood to mirror the corresponding profile in the target tissue.

  14. The epigenomics of polycystic ovarian syndrome: from pathogenesis to clinical manifestations.

    Science.gov (United States)

    Li, Shuxia; Zhu, Dongyi; Duan, Hongmei; Tan, Qihua

    2016-12-01

    Polycystic ovarian syndrome (PCOS) is a complex condition of ovarian dysfunction and metabolic abnormalities with widely varying clinical manifestations resulting from interference of the genome and the environment through integrative biological mechanisms with the emerging field of epigenetics offering an appealing tool for studying the nature and nurture of the disease. We review the current literature of epigenetic studies on PCOS from disease development to the association analysis of the DNA methylome and to exploratory studies on the molecular mechanisms of disease heterogeneity and comorbidity. Recent data based on profiling of the DNA methylome of PCOS in different tissues provided consistent molecular evidence in support of epidemiological findings on disease comorbidity suggesting a possible autoimmune basis in the pathogenesis of the disease. We show that the field of epigenetics and epigenomics could serve to link molecular regulatory mechanisms with disease development and disease manifestation which could contribute to PCOS prevention and treatment and eventually promote reproductive health in fertile age women. We summarize the up-to-date findings and discuss the implications of various studies and point to new avenues of research on PCOS in the rapidly developing field of epigenetics and epigenomics.

  15. Considering maternal dietary modulators for epigenetic regulation and programming of the fetal epigenome.

    Science.gov (United States)

    Chango, Abalo; Pogribny, Igor P

    2015-04-14

    Fetal life is characterized by a tremendous plasticity and ability to respond to various environmental and lifestyle factors, including maternal nutrition. Identification of the role of dietary factors that can modulate and reshape the cellular epigenome during development, including methyl group donors (e.g., folate, choline) and bioactive compounds (e.g., polyphenols) is of great importance; however, there is insufficient knowledge of a particular effect of each type of modulator and/or their combination on fetal life. To enhance the quality and safety of food products for proper fetal health and disease prevention in later life, a better understanding of the underlying mechanisms of dietary epigenetic modulators during the critical prenatal period is necessary. This review focuses on the influence of maternal dietary components on DNA methylation, histone modification, and microRNAs, and summarizes current knowledge of the effect and importance of dietary components on epigenetic mechanisms that control the proper expression of genetic information. Evidence reveals that some components in the maternal diet can directly or indirectly affect epigenetic mechanisms. Understanding the underlying mechanisms of how early-life nutritional environment affects the epigenome during development is of great importance for the successful prevention of adult chronic diseases through optimal maternal nutrition.

  16. Communicating the Needs of Climate Change Policy Makers to Scientists

    Science.gov (United States)

    Brown, Molly E.; Escobar, Vanessa M.; Lovell, Heather

    2012-01-01

    This chapter will describe the challenges that earth scientists face in developing science data products relevant to decision maker and policy needs, and will describe strategies that can improve the two-way communication between the scientist and the policy maker. Climate change policy and decision making happens at a variety of scales - from local government implementing solar homes policies to international negotiations through the United Nations Framework Convention on Climate Change. Scientists can work to provide data at these different scales, but if they are not aware of the needs of decision makers or understand what challenges the policy maker is facing, they are likely to be less successful in influencing policy makers as they wished. This is because the science questions they are addressing may be compelling, but not relevant to the challenges that are at the forefront of policy concerns. In this chapter we examine case studies of science-policy partnerships, and the strategies each partnership uses to engage the scientist at a variety of scales. We examine three case studies: the global Carbon Monitoring System pilot project developed by NASA, a forest biomass mapping effort for Silvacarbon project, and a forest canopy cover project being conducted for forest management in Maryland. In each of these case studies, relationships between scientists and policy makers were critical for ensuring the focus of the science as well as the success of the decision-making.

  17. Inverting EPO: Pedagogy for Scientists

    Science.gov (United States)

    Johnson, K. E.

    2002-05-01

    ``Education and Public Outreach" has an increasingly important role in our field, and is critical to the continued levels of funding from congress. However, in our enthusiasm to interact with the public and improve undergraduate courses, many astronomers find themselves ``reinventing the wheel" in astronomy education. There are many fundamental principles in education with which scientists should be familiar before entering the classroom or engaging the public. In this talk I will overview a pedagogy course we are developing to give graduate students in astronomy a grounding in important and useful principles in education.

  18. A scientist at the seashore

    CERN Document Server

    Trefil, James S

    2005-01-01

    ""A marvelous excursion from the beach to the ends of the solar system . . . captivating.""-The New York Times""So easy to understand yet so dense with knowledge that you'll never look at waves on a beach the same way again.""-San Francisco Chronicle""One of the best popular science books.""-The Kansas City Star""Perfect for the weekend scientist.""-The Richmond News-LeaderA noted physicist and popular science writer heads for the beach to answer common and uncommon questions about the ocean. James S. Trefil, author of Dover Publications' The Moment of Creation: Big Bang Physics from Before th

  19. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... Ask a Scientist Video Series Listen All About Vision About the Eye Ask a Scientist Video Series ... Eye Health and Safety First Aid Tips Healthy Vision Tips Protective Eyewear Sports and Your Eyes Fun ...

  20. Ask a Scientist: What is Color Blindness?

    Science.gov (United States)

    ... Stuff Cool Eye Tricks Links to More Information Optical Illusions Printables Ask a Scientist Video Series Why can’ ... a scientist? Click to Watch What is an optical illusion? Click to Watch What is color blindness? Click ...

  1. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... Stuff Cool Eye Tricks Links to More Information Optical Illusions Printables Ask a Scientist Video Series Why can’ ... a scientist? Click to Watch What is an optical illusion? Click to Watch What is color blindness? Click ...

  2. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... to More Information Optical Illusions Printables Ask a Scientist Video Series Why can’t you see colors ... like these and more with our Ask a Scientist video series. Dr. Sheldon Miller answers questions about ...

  3. Scientists Discover Sugar in Space

    Science.gov (United States)

    2000-06-01

    The prospects for life in the Universe just got sweeter, with the first discovery of a simple sugar molecule in space. The discovery of the sugar molecule glycolaldehyde in a giant cloud of gas and dust near the center of our own Milky Way Galaxy was made by scientists using the National Science Foundation's 12 Meter Telescope, a radio telescope on Kitt Peak, Arizona. "The discovery of this sugar molecule in a cloud from which new stars are forming means it is increasingly likely that the chemical precursors to life are formed in such clouds long before planets develop around the stars," said Jan M. Hollis of the NASA Goddard Space Flight Center in Greenbelt, MD. Hollis worked with Frank J. Lovas of the University of Illinois and Philip R. Jewell of the National Radio Astronomy Observatory (NRAO) in Green Bank, WV, on the observations, made in May. The scientists have submitted their results to the Astrophysical Journal Letters. "This discovery may be an important key to understanding the formation of life on the early Earth," said Jewell. Conditions in interstellar clouds may, in some cases, mimic the conditions on the early Earth, so studying the chemistry of interstellar clouds may help scientists understand how bio-molecules formed early in our planet's history. In addition, some scientists have suggested that Earth could have been "seeded" with complex molecules by passing comets, made of material from the interstellar cloud that condensed to form the Solar System. Glycolaldehyde, an 8-atom molecule composed of carbon, oxygen and hydrogen, can combine with other molecules to form the more-complex sugars Ribose and Glucose. Ribose is a building block of nucleic acids such as RNA and DNA, which carry the genetic code of living organisms. Glucose is the sugar found in fruits. Glycolaldehyde contains exactly the same atoms, though in a different molecular structure, as methyl formate and acetic acid, both of which were detected previously in interstellar clouds

  4. Young scientists in the making

    CERN Multimedia

    Corinne Pralavorio

    2011-01-01

    Some 700 local primary-school children will be trying out the scientific method for themselves from February to June. After "Draw me a physicist", the latest project "Dans la peau d’un chercheur" ("Be a scientist for a day") is designed to give children a taste of what it's like to be a scientist. Both schemes are the fruit of a partnership between CERN, "PhysiScope" (University of Geneva) and the local education authorities in the Pays de Gex and the Canton of Geneva.   Juliette Davenne (left) and Marie Bugnon (centre) from CERN's Communication Group prepare the mystery boxes for primary schools with Olivier Gaumer (right) of PhysiScope. Imagine a white box that rattles and gives off a strange smell when you shake it… How would you go about finding out what's inside it without opening it? Thirty primary-school teachers from the Pays de Gex and the Canton of Geneva tried out this exercise on Wednesday 26 ...

  5. Students work as scientists for the summer

    DEFF Research Database (Denmark)

    Ryde, Marianne Vang

    2006-01-01

    Each year, Risø offers its PhD students a course to challenge the natural scientists of the future and to provide them with a more balanced view of their own role as scientists in society.......Each year, Risø offers its PhD students a course to challenge the natural scientists of the future and to provide them with a more balanced view of their own role as scientists in society....

  6. The Scientist in Society: Perspectives from Drama.

    Science.gov (United States)

    Brouwer, Wytze

    1990-01-01

    Discussed is whether scientists should take responsibility for the social consequences of their discoveries. Reviewed is the role to which the "modern" playwright assigns scientists in modern society and what might realistically be a role that scientists and scientific societies should play in the modern world. (KR)

  7. Power of Indian women scientists unravelled

    Indian Academy of Sciences (India)

    asura

    EVERY time you think of women scientists, you can't help but think of. Marie Curie or Dorothy. Hodgkin. In fact, how many of us even know that women scientists in India have made important con- tributions to science? In order to highlight the achievements of. Indian women scientists, the. Indian Academy of. Science,.

  8. Scientists Talking to Students through Videos

    Science.gov (United States)

    Chen, Junjun; Cowie, Bronwen

    2014-01-01

    The benefits of connecting school students with scientists are well documented. This paper reports how New Zealand teachers brought scientists into the classrooms through the use of videos of New Zealand scientists talking about themselves and their research. Two researchers observed lessons in 9 different classrooms in which 23 educational videos…

  9. Helping Young People Engage with Scientists

    Science.gov (United States)

    Leggett, Maggie; Sykes, Kathy

    2014-01-01

    There can be multiple benefits of scientists engaging with young people, including motivation and inspiration for all involved. But there are risks, particularly if scientists do not consider the interests and needs of young people or listen to what they have to say. We argue that "dialogue" between scientists, young people and teachers…

  10. Still Persistent Global Problem of Scientists' Image

    Science.gov (United States)

    Türkmen, Hakan

    2015-01-01

    Pre-service teachers' views of science and scientists have been widely studied. The purpose of this study is to identify whether there is problem of image of scientists and determine where they receive about scientist image. Three hundred thirty five (105 from Turkey, 162 from Europe, 68 from US) elementary pre-service teachers participated in…

  11. Spatial and Functional Relationships Among Pol V-Associated loci, Pol IV-Dependent siRNAs, and Cytosine Methylation in the Arabidopsis Epigenome

    Energy Technology Data Exchange (ETDEWEB)

    Wierzbicki, A. T.; Cocklin, Ross; Mayampurath, Anoop; Lister, Ryan; Rowley, M. J.; Gregory, Brian D.; Ecker, Joseph R.; Tang, Haixu; Pikaard, Craig S.

    2012-08-15

    Multisubunit RNA polymerases IV and V (Pols IV and V) mediate RNA-directed DNA methylation and transcriptional silencing of retrotransposons and heterochromatic repeats in plants. We identified genomic sites of Pol V occupancy in parallel with siRNA deep sequencing and methylcytosine mapping, comparing wild-type plants with mutants defective for Pol IV, Pol V, or both Pols IV and V. Approximately 60% of Pol V-associated regions encompass regions of 24-nucleotide (nt) siRNA complementarity and cytosine methylation, consistent with cytosine methylation being guided by base-pairing of Pol IV-dependent siRNAs with Pol V transcripts. However, 27% of Pol V peaks do not overlap sites of 24-nt siRNA biogenesis or cytosine methylation, indicating that Pol V alone does not specify sites of cytosine methylation. Surprisingly, the number of methylated CHH motifs, a hallmark of RNA-directed de novo methylation, is similar in wild-type plants and Pol IV or Pol V mutants. In the mutants, methylation is lost at 50%-60% of the CHH sites that are methylated in the wild type but is gained at new CHH positions, primarily in pericentromeric regions. These results indicate that Pol IV and Pol V are not required for cytosine methyltransferase activity but shape the epigenome by guiding CHH methylation to specific genomic sites.

  12. Effects of prenatal exposure to endocrine disruptors and toxic metals on the fetal epigenome

    Science.gov (United States)

    Bommarito, Paige A; Martin, Elizabeth; Fry, Rebecca C

    2017-01-01

    Exposure to environmental contaminants during pregnancy has been linked to adverse outcomes at birth and later in life. The link between prenatal exposures and latent health outcomes suggests that these exposures may result in long-term epigenetic reprogramming. Toxic metals and endocrine disruptors are two major classes of contaminants that are ubiquitously present in the environment and represent threats to human health. In this review, we present evidence that prenatal exposures to these contaminants result in fetal epigenomic changes, including altered global DNA methylation, gene-specific CpG methylation and microRNA expression. Importantly, these changes may have functional cellular consequences, impacting health outcomes later in life. Therefore, these epigenetic changes represent a critical mechanism that warrants further study. PMID:28234024

  13. The epigenomics of polycystic ovarian syndrome: from pathogenesis to clinical manifestations

    DEFF Research Database (Denmark)

    Li, Shuxia; Zhu, Dongyi; Duan, Hongmei

    2016-01-01

    Polycystic ovarian syndrome (PCOS) is a complex condition of ovarian dysfunction and metabolic abnormalities with widely varying clinical manifestations resulting from interference of the genome and the environment through integrative biological mechanisms with the emerging field of epigenetics...... offering an appealing tool for studying the nature and nurture of the disease. We review the current literature of epigenetic studies on PCOS from disease development to the association analysis of the DNA methylome and to exploratory studies on the molecular mechanisms of disease heterogeneity...... and epigenomics could serve to link molecular regulatory mechanisms with disease development and disease manifestation which could contribute to PCOS prevention and treatment and eventually promote reproductive health in fertile age women. We summarize the up-to-date findings and discuss the implications...

  14. Epigenomic strategies at the interface of genetic and environmental risk factors for autism.

    Science.gov (United States)

    LaSalle, Janine M

    2013-07-01

    Autism spectrum disorders (ASD) have been increasing in prevalence over the last two decades, primarily because of increased awareness and diagnosis. However, autism is clearly a complex human genetic disorder that involves interactions between genes and environment. Epigenetic mechanisms, such as DNA methylation, act at the interface of genetic and environmental risk and protective factors. Advancements in genome-wide sequencing has broadened the view of the human methylome and revealed the organization of the human genome into large-scale methylation domains that footprint over neurologically important genes involved in embryonic development. Future integrative epigenomic analyses of genetic risk factors with environmental exposures and methylome analyses are expected to be important for understanding the complex etiology of ASD.

  15. Single-cell epigenomics: Recording the past and predicting the future.

    Science.gov (United States)

    Kelsey, Gavin; Stegle, Oliver; Reik, Wolf

    2017-10-06

    Single-cell multi-omics has recently emerged as a powerful technology by which different layers of genomic output-and hence cell identity and function-can be recorded simultaneously. Integrating various components of the epigenome into multi-omics measurements allows for studying cellular heterogeneity at different time scales and for discovering new layers of molecular connectivity between the genome and its functional output. Measurements that are increasingly available range from those that identify transcription factor occupancy and initiation of transcription to long-lasting and heritable epigenetic marks such as DNA methylation. Together with techniques in which cell lineage is recorded, this multilayered information will provide insights into a cell's past history and its future potential. This will allow new levels of understanding of cell fate decisions, identity, and function in normal development, physiology, and disease. Copyright © 2017, American Association for the Advancement of Science.

  16. MethCNA: a database for integrating genomic and epigenomic data in human cancer.

    Science.gov (United States)

    Deng, Gaofeng; Yang, Jian; Zhang, Qing; Xiao, Zhi-Xiong; Cai, Haoyang

    2018-02-13

    The integration of DNA methylation and copy number alteration data promises to provide valuable insight into the underlying molecular mechanisms responsible for cancer initiation and progression. However, the generation and processing of these datasets are costly and time-consuming if carried out separately. The Illumina Infinium HumanMethylation450 BeadChip, initially designed for the evaluation of DNA methylation levels, allows copy number variant calling using bioinformatics tools. A substantial amount of Infinium HumanMethylation450 data across various cancer types has been accumulated in recent years and is a valuable resource for large-scale data analysis. Here we present MethCNA, a comprehensive database for genomic and epigenomic data integration in human cancer. In the current release, MethCNA contains about 10,000 tumor samples representing 37 cancer types. All raw array data were collected from The Cancer Genome Atlas and NCBI Gene Expression Omnibus database and analyzed using a pipeline that integrated multiple computational resources and tools. The normalized copy number aberration data and DNA methylation alterations were obtained. We provide a user-friendly web-interface for data mining and visualization. The Illumina Infinium HumanMethylation450 BeadChip enables the interrogation and integration of both genomic and epigenomic data from exactly the same DNA specimen, and thus can aid in distinguishing driver from passenger mutations in cancer. We expect MethCNA will enable researchers to explore DNA methylation and copy number alteration patterns, identify key oncogenic drivers in cancer, and assist in the development of targeted therapies. MethCNA is publicly available online at http://cgma.scu.edu.cn/MethCNA .

  17. Wide Field Instrument Adjutant Scientist

    Science.gov (United States)

    Spergel, David

    As Wide Field Instrument Adjutant Scientist, my goal will be to maximize the science capability of the mission in a cost-contained environment. I hope to work with the HQ, project and the FSWG to assure mission success. I plan to play a leadership role in communicating the WFIRST science capabilities to the astronomy community , obtain input from both science teams and the broader community that help derive performance requirements and calibration metrics. I plan to focus on developing the observing program for the deep fields and focus on using them to calibrate instrument performance and capabilities. I plan to organize workshops that will bring together WFIRST team members with astronomers working on LSST, Euclid, JWST, and the ELTs to maximize combined science return. I am also eager to explore the astrometric and stellar seismology capabilities of the instrument with a goal of maximizing science return without affecting science requirements.

  18. Data Scientist Training for Librarians

    Science.gov (United States)

    Erdmann, C.

    2015-04-01

    Recent studies suggest that there will be a shortfall in the near future of skilled talent available to help take advantage of big data in organizations. Meanwhile, government initiatives have encouraged the research community to share their data more openly, raising new challenges for researchers. Librarians can assist in this new data-driven environment. Data Scientist Training for Librarians (or Data Savvy Librarians) is an experimental course being offered by the Harvard Library to train librarians to respond to the growing data needs of their communities. In the course, librarians familiarize themselves with the research data lifecycle, working hands-on with the latest tools for extracting, wrangling, storing, analyzing, and visualizing data. By experiencing the research data lifecycle themselves, and becoming data savvy and embracing the data science culture, librarians can begin to imagine how their services might be transformed.

  19. Refugee scientists and nuclear energy

    International Nuclear Information System (INIS)

    Segre, E.

    1985-01-01

    The coming together of many of the world's experts in nuclear physics in the 1930's was largely the result of the persecution of Jews in Germany and later in Italy. Initially this meant there were no jobs for young physicists to go into as the senior scientists had been sacked. Later, it resulted in the assembly of many of the world's foremost physicists in the United States, specifically at the Los Alamos Laboratory to work on the Manhattan Project. The rise of antisemitism in Italy (to where many physicists had fled at first) provoked the emigration of Fermi, the leading expert on neutrons at that time. The politics, physics and personalities in the 1930's, relevant to the development of nuclear energy, are discussed. (UK)

  20. Is evaluation of scientist's objective

    CERN Document Server

    Wold, A

    2000-01-01

    There is ample data demonstrating that female scientists advance at a far slower rate than their male colleagues. The low numbers of female professors in European and North American universities is, thus, not solely an effect of few women in the recruitment pool but also to obstacles specific to the female gender. Together with her colleague Christine Wennerås, Agnes Wold conducted a study of the evaluation process at the Swedish Medical Research Council. Evaluators judged the "scientific competence", "research proposal" and "methodology" of applicants for post-doctoral positions in 1995. By relating the scores for "scientific competence" to the applicants' scientific productivity and other factors using multiple regression, Wennerås and Wold demonstrated that the applicant's sex exerted a strong influence on the "competence" score so that male applicants were perceived as being more competent than female applicants of equal productivity. The study was published in Nature (vol 387, p 341-3, 1997) and inspir...

  1. LHCb Early Career Scientist Awards

    CERN Multimedia

    Patrick Koppenburg for the LHCb Collaboration

    2016-01-01

    On 15 September 2016, the LHCb collaboration awarded the first set of prizes for outstanding contributions of early career scientists.   From left to right: Guy Wilkinson (LHCb spokesperson), Sascha Stahl, Kevin Dungs, Tim Head, Roel Aaij, Conor Fitzpatrick, Claire Prouvé, Patrick Koppenburg (chair of committee) and Sean Benson. Twenty-five nominations were submitted and considered by the committee, and 5 prizes were awarded to teams or individuals for works that had a significant impact within the last year. The awardees are: Roel Aaij, Sean Benson, Conor Fitzpatrick, Rosen Matev and Sascha Stahl for having implemented and commissioned the revolutionary changes to the LHC Run-2 high-level-trigger, including the first widespread deployment of real-time analysis techniques in High Energy Physics;   Kevin Dungs and Tim Head for having launched the Starterkit initiative, a new style of software tutorials based on modern programming methods. “Starterkit is a group of ph...

  2. Multi-ethnic fine-mapping of 14 central adiposity loci

    DEFF Research Database (Denmark)

    Liu, Ching-Ti; Buchkovich, Martin L; Winkler, Thomas W

    2014-01-01

    The Genetic Investigation of Anthropometric Traits (GIANT) consortium identified 14 loci in European Ancestry (EA) individuals associated with waist-to-hip ratio (WHR) adjusted for body mass index. These loci are wide and narrowing the signals remains necessary. Twelve of 14 loci identified in GI......-analysis results and aids in fine-mapping shared variants at these locations. We annotated variants using information from the ENCODE Consortium and Roadmap Epigenomics Project to prioritize variants for possible functionality....

  3. Meet the Scientist: The Value of Short Interactions between Scientists and Students

    Science.gov (United States)

    Woods-Townsend, Kathryn; Christodoulou, Andri; Rietdijk, Willeke; Byrne, Jenny; Griffiths, Janice B.; Grace, Marcus M.

    2016-01-01

    Students have been reported to have stereotypical views of scientists as middle-aged white men in lab coats. We argue that a way to provide students with a more realistic view of scientists and their work is to provide them with the opportunity to interact with scientists during short, discussion-based sessions. For that reason, 20 scientists from…

  4. Crowdsourcing The National Map

    Science.gov (United States)

    McCartney, Elizabeth; Craun, Kari J.; Korris, Erin M.; Brostuen, David A.; Moore, Laurence R.

    2015-01-01

    Using crowdsourcing techniques, the US Geological Survey’s (USGS) Volunteered Geographic Information (VGI) project known as “The National Map Corps (TNMCorps)” encourages citizen scientists to collect and edit data about man-made structures in an effort to provide accurate and authoritative map data for the USGS National Geospatial Program’s web-based The National Map. VGI is not new to the USGS, but past efforts have been hampered by available technologies. Building on lessons learned, TNMCorps volunteers are successfully editing 10 different structure types in all 50 states as well as Puerto Rico and the US Virgin Islands.

  5. Drought Information Supported by Citizen Scientists (DISCS)

    Science.gov (United States)

    Molthan, A.; Maskey, M.; Hain, C.; Meyer, P.; Nair, U. S.; Handyside, C. T.; White, K.; Amin, M.

    2017-12-01

    Each year, drought impacts various regions of the United States on time scales of weeks, months, seasons, or years, which in turn leads to a need to document these impacts and inform key decisions on land management, use of water resources, and disaster response. Mapping impacts allows decision-makers to understand potential damage to agriculture and loss of production, to communicate and document drought impacts on crop yields, and to inform water management decisions. Current efforts to collect this information includes parsing of media reports, collaborations with local extension offices, and partnerships with the National Weather Service cooperative observer network. As part of a NASA Citizen Science for Earth Systems proposal award, a research and applications team from Marshall Space Flight Center, the University of Alabama in Huntsville, and collaborators within the NWS have developed a prototype smartphone application focused on the collection of citizen science observations of crop health and drought impacts, along with development of innovative low-cost soil moisture sensors to supplement subjective assessments of local soil moisture conditions. Observations provided by citizen scientists include crop type and health, phase of growth, soil moisture conditions, irrigation status, along with an optional photo and comment to provide visual confirmation and other details. In exchange for their participation, users of the app also have access to unique land surface modeling data sets produced at MSFC such as the NASA Land Information System soil moisture and climatology/percentile products from the Short-term Prediction Research and Transition (SPoRT) Center, assessments of vegetation health and stress from NASA and NOAA remote sensing platforms (e.g. MODIS/VIIRS), outputs from a crop stress model developed at the University of Alabama in Huntsville, recent rainfall estimates from the NOAA/NWS network of ground-based weather radars, and other observations made

  6. Fourth international circumpolar arctic vegetation mapping workshop

    Science.gov (United States)

    Raynolds, Martha K.; Markon, C.J.

    2002-01-01

    During the week of April 10, 2001, the Fourth International Circumpolar Arctic Vegetation Mapping Workshop was held in Moscow, Russia. The purpose of this meeting was to bring together the vegetation scientists working on the Circumpolar Arctic Vegetation Map (CAVM) to (1) review the progress of current mapping activities, (2) discuss and agree upon a standard set of arctic tundra subzones, (3) plan for the production and dissemination of a draft map, and (4) begin work on a legend for the final map.

  7. EGU's Early Career Scientists Network

    Science.gov (United States)

    Roberts Artal, L.; Rietbroek, R.

    2017-12-01

    The EGU encourages early career scientists (ECS) to become involved in interdisciplinary research in the Earth, planetary and space sciences, through sessions, social events and short courses at the annual General Assembly in April and throughout the year. Through division-level representatives, all ECS members can have direct input into matters of the division. A Union-wide representative, who sits on the EGU Council, ensures that ECS are heard at a higher level in the Union too. After a brief introduction as to how the network is organised and structured, this presentation will discuss how EGU ECS activities have been tailored to the needs of ECS members and how those needs have been identified. Reaching and communicating opportunities to ECS remains an ongoing challenge; they will be discussed in this presentation too, as well as some thoughts on how to make them more effective. Finally, the service offered to EGU ECS members would certainly benefit from building links and collaboration with other early career networks in the geosciences. This presentation will outline some of our efforts in that direction and the challenges that remain.

  8. Transcriptional provirus silencing as a crosstalk of de novo DNA methylation and epigenomic features at the integration site

    Czech Academy of Sciences Publication Activity Database

    Šenigl, Filip; Auxt, Miroslav; Hejnar, Jiří

    2012-01-01

    Roč. 40, č. 12 (2012), s. 5298-5312 ISSN 0305-1048 R&D Projects: GA ČR GP301/09/P667; GA ČR GAP502/11/2207 Institutional research plan: CEZ:AV0Z50520514 Keywords : retrovirus integration * provirus silencing * epigenomics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.278, year: 2012

  9. Impact of body size, nutrition and socioeconomic position in early life on the epigenome: a systematic review protocol

    OpenAIRE

    Maddock, Jane; Wulaningsih, Wahyu; Hardy, Rebecca

    2017-01-01

    Background Body size, nutrition and socioeconomic position (SEP) in early life have been associated with a range of later life health outcomes. Epigenetic regulation is one mechanism through which these early life factors may impact later life health. The aim of this review protocol is to outline procedures to document the influence of body size, nutrition and SEP in early life on the epigenome. Methods MEDLINE, Embase and BIOSIS will be systematically searched using pre-defined keywords. Add...

  10. What Is the (ethical) Role of Scientists?

    Science.gov (United States)

    Oreskes, N.

    2014-12-01

    Many scientists are reluctant to speak out on issues of broad societal importance for fear that doing so crosses into territory that is not the scientists' domain. Others fear that scientists lose credibility when they address ethical and moral issues. A related concern is that discussing social or ethical questions runs the risk of politicizing science. Yet history shows that in the past, scientists often have spoken out on broad issues of societal concern, often (although not always) effectively. This paper explores the conditions under which scientists may be effective spokesmen and women on ethical and moral choices, and suggests some criteria by which scientists might decide when and whether it is appropriate for them to speak out beyond the circles of other technical experts.

  11. Gifted and Talented Students’ Images of Scientists

    Directory of Open Access Journals (Sweden)

    Sezen Camcı-Erdoğan

    2013-06-01

    Full Text Available The purpose of this study was to investigate gifted students’ images of scientists. The study involved 25 students in grades 7 and 8. The Draw-a-Scientist Test (DAST (Chamber, 183 was used to collect data. Drawings were eval-uated using certain criterion such as a scien-tist’s appearance and investigation, knowledge and technology symbols and gender and working style, place work, expressions, titles-captions-symbols and alternative images and age. The results showed that gifted students’ perceptions about scientists were stereotypical, generally with glasses and laboratory coats and working with experiment tubes, beakers indoors and using books, technological tools and dominantly lonely males. Most gifted stu-dents drew male scientists. Although females drew male scientists, none of the boys drew female scientist.

  12. Scientists' personality, values, and well-being.

    Science.gov (United States)

    Sato, Wataru

    2016-01-01

    Scientists play an important role in modern society. However, only a small number of their psychological characteristics, such as personality traits, have been investigated; hence, further investigation is required. In this study, scientists (n = 24) and non-scientist controls (n = 26) were assessed with respect to their five-factor personality traits, 10 basic values, and subjective well-being (subjective happiness and sense of purpose in life). Compared with the non-scientist control group and with normative data of laypeople, the scientists consistently exhibited greater openness (i.e., traits related to curiosity and intelligence), self-direction (i.e., values related to the pursuit of curiosity, creativity, and autonomous action), happiness, and sense of purpose in life. These data indicate that scientists possess personality traits and values suitable for a career in science, from which they also derive subjective well-being.

  13. Frederic Joliot-Curie, a tormented scientist

    International Nuclear Information System (INIS)

    Pinault, M.

    2000-01-01

    This article is a short biography of the French scientist Frederic Joliot-Curie. His fight for a peaceful use of atomic energy, his responsibilities as nuclear physicist and as the first director of the French atomic commission (CEA) have led him to face contradictions very difficult to manage. All along his career as a scientist and as a high ranked civil servant, F.Joliot-Curie tried to find an ethical way for scientists in modern societies. (A.C.)

  14. Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes.

    Science.gov (United States)

    Verkest, Aurine; Byzova, Marina; Martens, Cindy; Willems, Patrick; Verwulgen, Tom; Slabbinck, Bram; Rombaut, Debbie; Van de Velde, Jan; Vandepoele, Klaas; Standaert, Evi; Peeters, Marrit; Van Lijsebettens, Mieke; Van Breusegem, Frank; De Block, Marc

    2015-08-01

    To increase both the yield potential and stability of crops, integrated breeding strategies are used that have mostly a direct genetic basis, but the utility of epigenetics to improve complex traits is unclear. A better understanding of the status of the epigenome and its contribution to agronomic performance would help in developing approaches to incorporate the epigenetic component of complex traits into breeding programs. Starting from isogenic canola (Brassica napus) lines, epilines were generated by selecting, repeatedly for three generations, for increased energy use efficiency and drought tolerance. These epilines had an enhanced energy use efficiency, drought tolerance, and nitrogen use efficiency. Transcriptome analysis of the epilines and a line selected for its energy use efficiency solely revealed common differentially expressed genes related to the onset of stress tolerance-regulating signaling events. Genes related to responses to salt, osmotic, abscisic acid, and drought treatments were specifically differentially expressed in the drought-tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine-4 of histone 3, further supported the phenotype by targeting drought-responsive genes and facilitating the transcription of the differentially expressed genes. From these results, we conclude that the canola epigenome can be shaped by selection to increase energy use efficiency and stress tolerance. Hence, these findings warrant the further development of strategies to incorporate epigenetics into breeding. © 2015 American Society of Plant Biologists. All Rights Reserved.

  15. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project.

    Directory of Open Access Journals (Sweden)

    Vardhman K Rakyan

    2004-12-01

    Full Text Available The Human Epigenome Project aims to identify, catalogue, and interpret genome-wide DNA methylation phenomena. Occurring naturally on cytosine bases at cytosine-guanine dinucleotides, DNA methylation is intimately involved in diverse biological processes and the aetiology of many diseases. Differentially methylated cytosines give rise to distinct profiles, thought to be specific for gene activity, tissue type, and disease state. The identification of such methylation variable positions will significantly improve our understanding of genome biology and our ability to diagnose disease. Here, we report the results of the pilot study for the Human Epigenome Project entailing the methylation analysis of the human major histocompatibility complex. This study involved the development of an integrated pipeline for high-throughput methylation analysis using bisulphite DNA sequencing, discovery of methylation variable positions, epigenotyping by matrix-assisted laser desorption/ionisation mass spectrometry, and development of an integrated public database available at http://www.epigenome.org. Our analysis of DNA methylation levels within the major histocompatibility complex, including regulatory exonic and intronic regions associated with 90 genes in multiple tissues and individuals, reveals a bimodal distribution of methylation profiles (i.e., the vast majority of the analysed regions were either hypo- or hypermethylated, tissue specificity, inter-individual variation, and correlation with independent gene expression data.

  16. DNA Methylation Profiling of the Human Major Histocompatibility Complex: A Pilot Study for the Human Epigenome Project

    Science.gov (United States)

    Rakyan, Vardhman K; Hildmann, Thomas; Novik, Karen L; Lewin, Jörn; Tost, Jörg; Cox, Antony V; Andrews, T. Dan; Howe, Kevin L; Otto, Thomas; Olek, Alexander; Fischer, Judith; Gut, Ivo G; Berlin, Kurt

    2004-01-01

    The Human Epigenome Project aims to identify, catalogue, and interpret genome-wide DNA methylation phenomena. Occurring naturally on cytosine bases at cytosine–guanine dinucleotides, DNA methylation is intimately involved in diverse biological processes and the aetiology of many diseases. Differentially methylated cytosines give rise to distinct profiles, thought to be specific for gene activity, tissue type, and disease state. The identification of such methylation variable positions will significantly improve our understanding of genome biology and our ability to diagnose disease. Here, we report the results of the pilot study for the Human Epigenome Project entailing the methylation analysis of the human major histocompatibility complex. This study involved the development of an integrated pipeline for high-throughput methylation analysis using bisulphite DNA sequencing, discovery of methylation variable positions, epigenotyping by matrix-assisted laser desorption/ionisation mass spectrometry, and development of an integrated public database available at http://www.epigenome.org. Our analysis of DNA methylation levels within the major histocompatibility complex, including regulatory exonic and intronic regions associated with 90 genes in multiple tissues and individuals, reveals a bimodal distribution of methylation profiles (i.e., the vast majority of the analysed regions were either hypo- or hypermethylated), tissue specificity, inter-individual variation, and correlation with independent gene expression data. PMID:15550986

  17. DNA methylation in childhood asthma: an epigenome-wide meta-analysis.

    Science.gov (United States)

    Xu, Cheng-Jian; Söderhäll, Cilla; Bustamante, Mariona; Baïz, Nour; Gruzieva, Olena; Gehring, Ulrike; Mason, Dan; Chatzi, Leda; Basterrechea, Mikel; Llop, Sabrina; Torrent, Maties; Forastiere, Francesco; Fantini, Maria Pia; Carlsen, Karin C Lødrup; Haahtela, Tari; Morin, Andréanne; Kerkhof, Marjan; Merid, Simon Kebede; van Rijkom, Bianca; Jankipersadsing, Soesma A; Bonder, Marc Jan; Ballereau, Stephane; Vermeulen, Cornelis J; Aguirre-Gamboa, Raul; de Jongste, Johan C; Smit, Henriette A; Kumar, Ashish; Pershagen, Göran; Guerra, Stefano; Garcia-Aymerich, Judith; Greco, Dario; Reinius, Lovisa; McEachan, Rosemary R C; Azad, Raf; Hovland, Vegard; Mowinckel, Petter; Alenius, Harri; Fyhrquist, Nanna; Lemonnier, Nathanaël; Pellet, Johann; Auffray, Charles; van der Vlies, Pieter; van Diemen, Cleo C; Li, Yang; Wijmenga, Cisca; Netea, Mihai G; Moffatt, Miriam F; Cookson, William O C M; Anto, Josep M; Bousquet, Jean; Laatikainen, Tiina; Laprise, Catherine; Carlsen, Kai-Håkon; Gori, Davide; Porta, Daniela; Iñiguez, Carmen; Bilbao, Jose Ramon; Kogevinas, Manolis; Wright, John; Brunekreef, Bert; Kere, Juha; Nawijn, Martijn C; Annesi-Maesano, Isabella; Sunyer, Jordi; Melén, Erik; Koppelman, Gerard H

    2018-02-26

    DNA methylation profiles associated with childhood asthma might provide novel insights into disease pathogenesis. We did an epigenome-wide association study to assess methylation profiles associated with childhood asthma. We did a large-scale epigenome-wide association study (EWAS) within the Mechanisms of the Development of ALLergy (MeDALL) project. We examined epigenome-wide methylation using Illumina Infinium Human Methylation450 BeadChips (450K) in whole blood in 207 children with asthma and 610 controls at age 4-5 years, and 185 children with asthma and 546 controls at age 8 years using a cross-sectional case-control design. After identification of differentially methylated CpG sites in the discovery analysis, we did a validation study in children (4-16 years; 247 cases and 2949 controls) from six additional European cohorts and meta-analysed the results. We next investigated whether replicated CpG sites in cord blood predict later asthma in 1316 children. We subsequently investigated cell-type-specific methylation of the identified CpG sites in eosinophils and respiratory epithelial cells and their related gene-expression signatures. We studied cell-type specificity of the asthma association of the replicated CpG sites in 455 respiratory epithelial cell samples, collected by nasal brushing of 16-year-old children as well as in DNA isolated from blood eosinophils (16 with asthma, eight controls [age 2-56 years]) and compared this with whole-blood DNA samples of 74 individuals with asthma and 93 controls (age 1-79 years). Whole-blood transcriptional profiles associated with replicated CpG sites were annotated using RNA-seq data of subsets of peripheral blood mononuclear cells sorted by fluorescence-activated cell sorting. 27 methylated CpG sites were identified in the discovery analysis. 14 of these CpG sites were replicated and passed genome-wide significance (ptranscriptional signatures associated with these CpG sites indicated increased activation of

  18. Integrative epigenomic analysis identifies biomarkers and therapeutic targets in adult B-acute lymphoblastic leukemia.

    Science.gov (United States)

    Geng, Huimin; Brennan, Sarah; Milne, Thomas A; Chen, Wei-Yi; Li, Yushan; Hurtz, Christian; Kweon, Soo-Mi; Zickl, Lynette; Shojaee, Seyedmehdi; Neuberg, Donna; Huang, Chuanxin; Biswas, Debabrata; Xin, Yuan; Racevskis, Janis; Ketterling, Rhett P; Luger, Selina M; Lazarus, Hillard; Tallman, Martin S; Rowe, Jacob M; Litzow, Mark R; Guzman, Monica L; Allis, C David; Roeder, Robert G; Müschen, Markus; Paietta, Elisabeth; Elemento, Olivier; Melnick, Ari M

    2012-11-01

    Genetic lesions such as BCR-ABL1, E2A-PBX1, and MLL rearrangements (MLLr) are associated with unfavorable outcomes in adult B-cell precursor acute lymphoblastic leukemia (B-ALL). Leukemia oncoproteins may directly or indirectly disrupt cytosine methylation patterning to mediate the malignant phenotype. We postulated that DNA methylation signatures in these aggressive B-ALLs would point toward disease mechanisms and useful biomarkers and therapeutic targets. We therefore conducted DNA methylation and gene expression profiling on a cohort of 215 adult patients with B-ALL enrolled in a single phase III clinical trial (ECOG E2993) and normal control B cells. In BCR-ABL1-positive B-ALLs, aberrant cytosine methylation patterning centered around a cytokine network defined by hypomethylation and overexpression of IL2RA(CD25). The E2993 trial clinical data showed that CD25 expression was strongly associated with a poor outcome in patients with ALL regardless of BCR-ABL1 status, suggesting CD25 as a novel prognostic biomarker for risk stratification in B-ALLs. In E2A-PBX1-positive B-ALLs, aberrant DNA methylation patterning was strongly associated with direct fusion protein binding as shown by the E2A-PBX1 chromatin immunoprecipitation (ChIP) sequencing (ChIP-seq), suggesting that E2A-PBX1 fusion protein directly remodels the epigenome to impose an aggressive B-ALL phenotype. MLLr B-ALL featured prominent cytosine hypomethylation, which was linked with MLL fusion protein binding, H3K79 dimethylation, and transcriptional upregulation, affecting a set of known and newly identified MLL fusion direct targets with oncogenic activity such as FLT3 and BCL6. Notably, BCL6 blockade or loss of function suppressed proliferation and survival of MLLr leukemia cells, suggesting BCL6-targeted therapy as a new therapeutic strategy for MLLr B-ALLs. We conducted the first integrative epigenomic study in adult B-ALLs, as a correlative study to the ECOG E2993 phase III clinical trial. This

  19. An epigenome-wide association study of total serum IgE in Hispanic children.

    Science.gov (United States)

    Chen, Wei; Wang, Ting; Pino-Yanes, Maria; Forno, Erick; Liang, Liming; Yan, Qi; Hu, Donglei; Weeks, Daniel E; Baccarelli, Andrea; Acosta-Perez, Edna; Eng, Celeste; Han, Yueh-Ying; Boutaoui, Nadia; Laprise, Catherine; Davies, Gwyneth A; Hopkin, Julian M; Moffatt, Miriam F; Cookson, William O C M; Canino, Glorisa; Burchard, Esteban G; Celedón, Juan C

    2017-08-01

    Total IgE is a therapeutic target in patients with allergic diseases. DNA methylation in white blood cells (WBCs) was associated with total IgE levels in an epigenome-wide association study of white subjects. Whether DNA methylation of eosinophils explains these findings is insufficiently understood. We tested for association between genome-wide DNA methylation in WBCs and total IgE levels in 2 studies of Hispanic children: the Puerto Rico Genetics of Asthma and Lifestyle Study (PR-GOAL; n = 306) and the Genes-environments and Admixture in Latino Americans (GALA II) study (n = 573). Whole-genome methylation of DNA from WBCs was measured by using the Illumina Infinium HumanMethylation450 BeadChip. Total IgE levels were measured by using the UniCAP 100 system. In PR-GOAL WBC types (ie, neutrophils, eosinophils, basophils, lymphocytes, and monocytes) in peripheral blood were measured by using Coulter Counter techniques. In the GALA II study WBC types were imputed. Multivariable linear regression was used for the analysis of DNA methylation and total IgE levels, which was first conducted separately for each cohort, and then results from the 2 cohorts were combined in a meta-analysis. CpG sites in multiple genes, including novel findings and results previously reported in white subjects, were significantly associated with total IgE levels. However, adjustment for WBC types resulted in markedly fewer significant sites. Top findings from this adjusted meta-analysis were in the genes ZFPM1 (P = 1.5 × 10 -12 ), ACOT7 (P = 2.5 × 10 -11 ), and MND1 (P = 1.4 × 10 -9 ). In an epigenome-wide association study adjusted for WBC types (including eosinophils), methylation changes in genes enriched in pathways relevant to asthma and immune responses were associated with total IgE levels among Hispanic children. Copyright © 2017 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  20. Preparing Planetary Scientists to Engage Audiences

    Science.gov (United States)

    Shupla, C. B.; Shaner, A. J.; Hackler, A. S.

    2017-12-01

    While some planetary scientists have extensive experience sharing their science with audiences, many can benefit from guidance on giving presentations or conducting activities for students. The Lunar and Planetary Institute (LPI) provides resources and trainings to support planetary scientists in their communication efforts. Trainings have included sessions for students and early career scientists at conferences (providing opportunities for them to practice their delivery and receive feedback for their poster and oral presentations), as well as separate communication workshops on how to engage various audiences. LPI has similarly begun coaching planetary scientists to help them prepare their public presentations. LPI is also helping to connect different audiences and their requests for speakers to planetary scientists. Scientists have been key contributors in developing and conducting activities in LPI education and public events. LPI is currently working with scientists to identify and redesign short planetary science activities for scientists to use with different audiences. The activities will be tied to fundamental planetary science concepts, with basic materials and simple modifications to engage different ages and audience size and background. Input from the planetary science community on these efforts is welcome. Current results and resources, as well as future opportunities will be shared.

  1. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... MSC 9300 Bethesda, MD 20892-9300 (Courier services use: Rockville, MD 20852) 301-451-2020 Research at ... Ask a Scientist Video Series Glossary The Visual System Your Eyes’ Natural Defenses Eye Health and Safety ... Ask a Scientist Video Series ...

  2. Code Review For and By Scientists

    OpenAIRE

    Petre, Marian; Wilson, Greg

    2014-01-01

    We describe two pilot studies of code review by and for scientists. Our principal findings are that scientists are enthusiastic, but need to be shown code review in action, and that just-in-time review of small code changes is more likely to succeed than large-scale end-of-work reviews.

  3. Chinese, US scientists find new particle

    CERN Multimedia

    2003-01-01

    "Chinese and US scientists have discovered a new particle at the Beijing Electron Position Collider, which is hard to be explained with any known particles, according to scientists from the Institute of High Energy Physics under the Chinese Academy of Sciences Wednesday" (1/2 page).

  4. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... Ask a Scientist Video Series Glossary The Visual System Your Eyes’ Natural Defenses Eye Health and Safety First Aid Tips Healthy Vision Tips Protective Eyewear Sports and Your Eyes Fun Stuff Cool Eye Tricks Links to More Information Optical Illusions Printables Ask a Scientist Video Series ...

  5. Tens of Romanian scientists work at CERN

    CERN Multimedia

    Silian, Sidonia

    2007-01-01

    "The figures regarding the actual number of Romanian scientists working at the European Center for Nuclear Research, or CERN, differ. The CERN data base lists some 30 Romanians on its payroll, while the scientists with the Nuclear Center at Magurele, Romania, say they should be around 50." (1 page)

  6. Scientists Like Me: Faces of Discovery

    Science.gov (United States)

    Enevoldsen, A. A. G.; Culp, S.; Trinh, A.

    2010-08-01

    During the International Year of Astronomy, Pacific Science Center is hosting a photography exhibit: Scientists Like Me: Faces of Discovery. The exhibit contains photographs of real, current astronomers and scientists working in astronomy and aerospace-related fields from many races, genders, cultural affiliations and walks of life. The photographs were taken and posters designed by Alyssa Trinh and Sarah Culp, high school interns in Discovery Corps, Pacific Science Center's youth development program. The direct contact between the scientists and the interns helps the intended audience of teachers and families personally connect with scientists. The finished posters from this exhibit are available online (http://pacificsciencecenter.org/scientists) for teachers to use in their classrooms, in addition to being displayed at Pacific Science Center and becoming part of Pacific Science Center's permanent art rotation. The objective of this project was to fill a need for representative photographs of scientists in the world community. It also met two of the goals of International Year of Astronomy: to provide a modern image of science and scientists, and to improve the gender-balanced representation of scientists at all levels and promote greater involvement by all people in scientific and engineering careers. We would like to build on the success of this project and create an annual summer internship, with different interns, focusing on creating posters for different fields of science.

  7. Code of conduct for scientists (abstract)

    International Nuclear Information System (INIS)

    Khurshid, S.J.

    2011-01-01

    The emergence of advanced technologies in the last three decades and extraordinary progress in our knowledge on the basic Physical, Chemical and Biological properties of living matter has offered tremendous benefits to human beings but simultaneously highlighted the need of higher awareness and responsibility by the scientists of 21 century. Scientist is not born with ethics, nor science is ethically neutral, but there are ethical dimensions to scientific work. There is need to evolve an appropriate Code of Conduct for scientist particularly working in every field of Science. However, while considering the contents, promulgation and adaptation of Codes of Conduct for Scientists, a balance is needed to be maintained between freedom of scientists and at the same time some binding on them in the form of Code of Conducts. The use of good and safe laboratory procedures, whether, codified by law or by common practice must also be considered as part of the moral duties of scientists. It is internationally agreed that a general Code of Conduct can't be formulated for all the scientists universally, but there should be a set of 'building blocks' aimed at establishing the Code of Conduct for Scientists either as individual researcher or responsible for direction, evaluation, monitoring of scientific activities at the institutional or organizational level. (author)

  8. Student Pugwash Conference Probes Scientists' Individual Responsibility.

    Science.gov (United States)

    Seltzer, Richard J.

    1985-01-01

    Students from 25 nations and senior scientists examined ethical and social dimensions of decision making about science and technology during the 1985 Student Pugwash Conference on scientists' individual responsibilities. Working groups focused on toxic wastes, military uses of space, energy and poverty, genetic engineering, and individual rights.…

  9. Response: Training Doctoral Students to Be Scientists

    Science.gov (United States)

    Pollio, David E.

    2012-01-01

    The purpose of this article is to begin framing doctoral training for a science of social work. This process starts by examining two seemingly simple questions: "What is a social work scientist?" and "How do we train social work scientists?" In answering the first question, some basic assumptions and concepts about what constitutes a "social work…

  10. Scientists' Views about Communication Training

    Science.gov (United States)

    Besley, John C.; Dudo, Anthony; Storksdieck, Martin

    2015-01-01

    This study assesses how scientists think about science communication training based on the argument that such training represents an important tool in improving the quality of interactions between scientists and the public. It specifically focuses on training related to five goals, including views about training to make science messages…

  11. Predicting scientists' participation in public life.

    Science.gov (United States)

    Besley, John C; Oh, Sang Hwa; Nisbet, Matthew

    2013-11-01

    This research provides secondary data analysis of two large-scale scientist surveys. These include a 2009 survey of American Association for the Advancement of Science (AAAS) members and a 2006 survey of university scientists by the United Kingdom's Royal Society. Multivariate models are applied to better understand the motivations, beliefs, and conditions that promote scientists' involvement in communication with the public and the news media. In terms of demographics, scientists who have reached mid-career status are more likely than their peers to engage in outreach, though even after controlling for career stage, chemists are less likely than other scientists to do so. In terms of perceptions and motivations, a deficit model view that a lack of public knowledge is harmful, a personal commitment to the public good, and feelings of personal efficacy and professional obligation are among the strongest predictors of seeing outreach as important and in participating in engagement activities.

  12. Genomic and epigenomic analyses of monozygotic twins discordant for congenital renal agenesis.

    Science.gov (United States)

    Jin, Meiling; Zhu, Shida; Hu, Panpan; Liu, Dongbing; Li, Qinggang; Li, Zuoxiang; Zhang, Xueguang; Xie, Yuansheng; Chen, Xiangmei

    2014-07-01

    Monozygotic twins have been widely studied to distinguish genetic and environmental factors in the pathogenesis of human diseases. For renal agenesis, the one-sided absence of renal tissue, the relative contributions of genetic and environmental factors to its pathogenesis are still unclear. In this study of a pair of monozygotic twins discordant for congenital renal agenesis, the genomic profile was analyzed from a set of blood samples using high-throughput exome-capture sequencing to detect single-nucleotide polymorphisms (SNPs), copy number variations (CNVs), and insertions and deletions (indels). Also, an epigenomic analysis used reduced-representation bisulfite sequencing to detect differentially methylated regions (DMRs). No discordant SNPs, CNVs, or indels were confirmed, but 514 DMRs were detected. KEGG analysis indicated the DMRs localized to 10 signaling pathways and 25 genes, including the mitogen-activated protein kinase pathway and 6 genes (FGF18, FGF12, PDGFRA, MAPK11, AMH, CTBP1) involved in organ development. Although methylation results from our adult patient and her sister may not represent the pattern that was present during kidney development, we could at least confirm a lack of obvious differences at the genome level, which suggests that nongenetic factors may be involved in the pathogenesis of renal agenesis. Copyright © 2014 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

  13. Naked Mole Rat Cells Have a Stable Epigenome that Resists iPSC Reprogramming

    Directory of Open Access Journals (Sweden)

    Li Tan

    2017-11-01

    Full Text Available Naked mole rat (NMR is a valuable model for aging and cancer research due to its exceptional longevity and cancer resistance. We observed that the reprogramming efficiency of NMR fibroblasts in response to OSKM was drastically lower than that of mouse fibroblasts. Expression of SV40 LargeT antigen (LT dramatically improved reprogramming of NMR fibroblasts. Inactivation of Rb alone, but not p53, was sufficient to improve reprogramming efficiency, suggesting that NMR chromatin may be refractory to reprogramming. Analysis of the global histone landscape revealed that NMR had higher levels of repressive H3K27 methylation marks and lower levels of activating H3K27 acetylation marks than mouse. ATAC-seq revealed that in NMR, promoters of reprogramming genes were more closed than mouse promoters, while expression of LT led to massive opening of the NMR promoters. These results suggest that NMR displays a more stable epigenome that resists de-differentiation, contributing to the cancer resistance and longevity of this species.

  14. An epigenomics approach to individual differences and its translation to neuropsychiatric conditions.

    Science.gov (United States)

    Sweatt, J David; Tamminga, Carol A

    2016-09-01

    This review concerns epigenetic mechanisms and their roles in conferring interindividual differences, especially as related to experientially acquired and genetically driven changes in central nervous system (CNS) function. In addition, the review contains commentary regarding the possible ways in which epigenomic changes may contribute to neuropsychiatric conditions and disorders and ways in which epigenotyping might be cross-correlated with clinical phenotyping in the context of precision medicine. The review begins with a basic description of epigenetic marking in the CNS and how these changes are powerful regulators of gene readout. Means for characterizing the individual epigenotype are briefly described, with a focus on DNA cytosine methylation as a readily measurable, stable epigenetic mark. This background enables a discussion of how "epigenotyping" might be integrated along with genotyping and deep phenotyping as a means of implementing advanced precision medicine. Finally, the commentary addresses two exemplars when considering how epigenotype may correlate with and modulate cognitive and behavioral phenotype: schizophrenia and Rett syndrome. These two disorders provide an interesting compare-and-contrast example regarding possible epigenotypic regulation of behavior: whereas Rett syndrome is clearly established as being caused by disruption of the function of an epigenetic "reader" of the DNA cytosine methylome-methyl-CpG-binding protein 2 (MeCP2)-the case for a role for epigenetic mechanisms in schizophrenia is still quite speculative.

  15. Novel Insights into Insect-Microbe Interactions- Role of Epigenomics and Small RNAs

    Directory of Open Access Journals (Sweden)

    Dohyup Kim

    2016-08-01

    Full Text Available It has become increasingly clear that microbes form close associations with the vast majority of animal species, especially insects. In fact, an array of diverse microbes is known to form shared metabolic pathways with their insect hosts. A growing area of research in insect-microbe interactions, notably for hemipteran insects and their mutualistic symbionts, is to elucidate the regulation of this inter domain metabolism. This review examines two new emerging mechanisms of gene regulation and their importance in host-microbe interactions. Specifically, we highlight how the incipient areas of research on regulatory 'dark matter' such as epigenomics and small RNAs, can play a pivotal role in the evolution of both insect and microbe gene regulation. We then propose specific models of how these dynamic forms of gene regulation can influence insect-symbiont-plant interactions. Future studies in this area of research will give us a systematic understanding of how these symbiotic microbes and animals reciprocally respond to, and regulate their shared metabolic processes.

  16. Epigenetic impact of dietary polyphenols in cancer chemoprevention: lifelong remodeling of our epigenomes.

    Science.gov (United States)

    Vanden Berghe, Wim

    2012-06-01

    Cancer, as one of the non-communicable diseases, remains one of the leading causes of death around the world. Recently, epigenetic changes in DNA methylation patterns at CpG sites (epimutations) or deregulated chromatin states of tumor promoting genes and noncoding RNAs emerged as major governing factors in tumor progression and cancer drug sensitivity. Furthermore, various environmental factors such as nutrition, behavior, stress, and toxins remodel our epigenomes lifelong in a beneficial or detrimental way. Since epigenetic marks (epimutations) are reversible in contrast to genetic defects, chemopreventive nutritional polyphenols (soy, genistein, resveratrol, catechin, curcumin) are currently evaluated for their ability to reverse adverse epigenetic marks in cancer (stem) cells to attenuate tumorigenesis-progression, prevent metastasis or sensitize for drug sensitivity. Although polyphenols in fruit and vegetables may help to reduce the risk of cancer, few protective effects have been firmly established, presumably because of inappropriate timing or dosing of diet exposure or due to confounding factors such as smoking and alcohol. In this review will discuss the possible epigenetic contributions of dietary polyphenols in cancer chemoprevention. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. Epigenomic mechanisms of early adversity and HPA dysfunction: Considerations for PTSD research

    Directory of Open Access Journals (Sweden)

    Patrick O McGowan

    2013-09-01

    Full Text Available Childhood adversity can have life-long consequences for the response to stressful events later in life. Abuse or severe neglect are well known risk factors for post-traumatic stress disorder (PTSD, at least in part via changes in neural systems mediating the endocrine response to stress. Determining the biological signatures of risk for stress-related mental disorders such as PTSD is important for identifying homogenous subgroups and improving treatment options. This review will focus on epigenetic regulation in early life by adversity and parental care – prime mediators of offspring neurodevelopment - in order to address several questions: (1 what have studies of humans and analogous animal models taught us about molecular mechanisms underlying changes in stress-sensitive physiological systems in response to early life trauma? (2 What are the considerations for studies relating early adversity and PTSD risk, going forward? I will summarize studies in animals and humans that address the epigenetic response to early adversity in the brain and in peripheral tissues. In so doing, I will describe work on the Glucocorticoid Receptor (GR and other well-characterized genes within the stress response pathway and then turn to genomic studies to illustrate the use of increasingly powerful high-throughput approaches to the study of epigenomic mechanisms.

  18. The toxicological application of transcriptomics and epigenomics in zebrafish and other teleosts.

    Science.gov (United States)

    Williams, Tim D; Mirbahai, Leda; Chipman, J Kevin

    2014-03-01

    Zebrafish (Danio rerio) is one of a number of teleost fish species frequently employed in toxicology. Toxico-genomics determines global transcriptomic responses to chemical exposures and can predict their effects. It has been applied successfully within aquatic toxicology to assist in chemical testing, determination of mechanisms and environmental monitoring. Moreover, the related field of toxico-epigenomics, that determines chemical-induced changes in DNA methylation, histone modifications and micro-RNA expression, is emerging as a valuable contribution to understanding mechanisms of both adaptive and adverse responses. Zebrafish has proven a useful and convenient model species for both transcriptomic and epigenetic toxicological studies. Despite zebrafish's dominance in other areas of fish biology, alternative fish species are used extensively in toxico-genomics. The main reason for this is that environmental monitoring generally focuses on species native to the region of interest. We are starting to see advances in the integration of high-throughput screening, omics techniques and bioinformatics together with more traditional indicator endpoints that are relevant to regulators. Integration of such approaches with high-throughput testing of zebrafish embryos, leading to the discovery of adverse outcome pathways, promises to make a major contribution to ensuring the safety of chemicals in the environment.

  19. Future of environmental research in the age of epigenomics and exposomics.

    Science.gov (United States)

    Holland, Nina

    2017-03-01

    Environmental research and public health in the 21st century face serious challenges such as increased air pollution and global warming, widespread use of potentially harmful chemicals including pesticides, plasticizers, and other endocrine disruptors, and radical changes in nutrition and lifestyle typical of modern societies. In particular, exposure to environmental and occupational toxicants may contribute to the occurrence of adverse birth outcomes, neurodevelopmental deficits, and increased risk of cancer and other multifactorial diseases such as diabetes and asthma. Rapidly evolving methodologies of exposure assessment and the conceptual framework of the Exposome, first introduced in 2005, are new frontiers of environmental research. Metabolomics and adductomics provide remarkable opportunities for a better understanding of exposure and prediction of potential adverse health outcomes. Metabolomics, the study of metabolism at whole-body level, involves assessment of the total repertoire of small molecules present in a biological sample, shedding light on interactions between gene expression, protein expression, and the environment. Advances in genomics, transcriptomics, and epigenomics are generating multidimensional structures of biomarkers of effect and susceptibility, increasingly important for the understanding of molecular mechanisms and the emergence of personalized medicine. Epigenetic mechanisms, particularly DNA methylation and miRNA expression, attract increasing attention as potential links between the genetic and environmental determinants of health and disease. Unlike genetics, epigenetic mechanisms could be reversible and an understanding of their role may lead to better protection of susceptible populations and improved public health.

  20. Analyzing Prospective Teachers' Images of Scientists Using Positive, Negative and Stereotypical Images of Scientists

    Science.gov (United States)

    Subramaniam, Karthigeyan; Harrell, Pamela Esprivalo; Wojnowski, David

    2013-01-01

    Background and purpose: This study details the use of a conceptual framework to analyze prospective teachers' images of scientists to reveal their context-specific conceptions of scientists. The conceptual framework consists of context-specific conceptions related to positive, stereotypical and negative images of scientists as detailed in the…

  1. Research to knowledge: promoting the training of physician-scientists in the biology of pregnancy.

    Science.gov (United States)

    Sadovsky, Yoel; Caughey, Aaron B; DiVito, Michelle; D'Alton, Mary E; Murtha, Amy P

    2018-01-01

    Common disorders of pregnancy, such as preeclampsia, preterm birth, and fetal growth abnormalities, continue to challenge perinatal biologists seeking insights into disease pathogenesis that will result in better diagnosis, therapy, and disease prevention. These challenges have recently been intensified with discoveries that associate gestational diseases with long-term maternal and neonatal outcomes. Whereas modern high-throughput investigative tools enable scientists and clinicians to noninvasively probe the maternal-fetal genome, epigenome, and other analytes, their implications for clinical medicine remain uncertain. Bridging these knowledge gaps depends on strengthening the existing pool of scientists with expertise in basic, translational, and clinical tools to address pertinent questions in the biology of pregnancy. Although PhD researchers are critical in this quest, physician-scientists would facilitate the inquiry by bringing together clinical challenges and investigative tools, promoting a culture of intellectual curiosity among clinical providers, and helping transform discoveries into relevant knowledge and clinical solutions. Uncertainties related to future administration of health care, federal support for research, attrition of physician-scientists, and an inadequate supply of new scholars may jeopardize our ability to address these challenges. New initiatives are necessary to attract current scholars and future generations of researchers seeking expertise in the scientific method and to support them, through mentorship and guidance, in pursuing a career that combines scientific investigation with clinical medicine. These efforts will promote breadth and depth of inquiry into the biology of pregnancy and enhance the pace of translation of scientific discoveries into better medicine and disease prevention. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... Disease Education Program Glaucoma Education Program Low Vision Education Program Hispanic/Latino ... a Scientist Video Series Glossary The Visual System Your Eyes’ Natural Defenses Eye Health and Safety ...

  3. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... Disease Education Program Glaucoma Education Program Low Vision Education Program ... Eye Ask a Scientist Video Series Glossary The Visual System Your Eyes’ Natural Defenses Eye Health and Safety ...

  4. Education and Outreach: Advice to Young Scientists

    Science.gov (United States)

    Lopes, R. M. C.

    2005-08-01

    Carl Sagan set an example to all scientists when he encouraged us to reach out to the public and share the excitement of discovery and exploration. The prejudice that ensued did not deter Sagan and, with the passing of years, more and more scientists have followed his example. Although at present scientists at all ranks are encouraged by their institutions to do outreach, the balancing of a successful scientific career with teaching and outreach is often not an easy one. Young scientists, in particular, may worry about how their outreach efforts are viewed in the community and how they will find the time and energy for these efforts. This talk will offer suggestions on how to balance an active science research program with outreach activities, the many different ways to engage in education and public outreach, and how the rewards are truly priceless.

  5. Women scientists reflections, challenges, and breaking boundaries

    CERN Document Server

    Hargittai, Magdolna

    2015-01-01

    Magdolna Hargittai uses over fifteen years of in-depth conversation with female physicists, chemists, biomedical researchers, and other scientists to form cohesive ideas on the state of the modern female scientist. The compilation, based on sixty conversations, examines unique challenges that women with serious scientific aspirations face. In addition to addressing challenges and the unjustifiable underrepresentation of women at the higher levels of academia, Hargittai takes a balanced approach by discussing how some of the most successful of these women have managed to obtain professional success and personal happiness. Women Scientists portrays scientists from different backgrounds, different geographical regions-eighteen countries from four continents-and leaders from a variety of professional backgrounds, including eight Nobel laureate women. The book is divided into three sections: "Husband and Wife Teams," "Women at the Top," and "In High Positions." Hargittai uses her own experience to introduce her fi...

  6. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... a Scientist Video Series Why can’t you see colors well in the dark? Do fish have ... sharper than a human’s. That means what you see clearly from five feet away, an eagle can ...

  7. Elements of ethics for physical scientists

    CERN Document Server

    Greer, Sandra C

    2017-01-01

    This book offers the first comprehensive guide to ethics for physical scientists and engineers who conduct research. Written by a distinguished professor of chemistry and chemical engineering, the book focuses on the everyday decisions about right and wrong faced by scientists as they do research, interact with other people, and work within society. The goal is to nurture readers’ ethical intelligence so that they know an ethical issue when they see one, and to give them a way to think about ethical problems. After introductions to the philosophy of ethics and the philosophy of science, the book discusses research integrity, with a unique emphasis on how scientists make mistakes and how they can avoid them. It goes on to cover personal interactions among scientists, including authorship, collaborators, predecessors, reviewers, grantees, mentors, and whistle-blowers. It considers underrepresented groups in science as an ethical issue that matters not only to those groups but also to the development of scien...

  8. Yelavarthy Nayudamma: Scientist, Leader, and Mentor Extraordinary

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 10. Yelavarthy Nayudamma: Scientist, Leader, and Mentor Extraordinary. J Raghava Rao T Ramasami. General Article Volume 19 Issue 10 October 2014 pp 887-899 ...

  9. CGH Short Term Scientist Exchange Program (STSEP)

    Science.gov (United States)

    STSEP promotes collaborative research between established U.S. and foreign scientists from low, middle, and upper-middle income countries (LMICs) by supporting, in part, exchange visits of cancer researchers between U.S. and foreign laboratories.

  10. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... Information Frequently asked questions Clinical Studies Publications Catalog Photos and Images Spanish Language Information Grants and Funding ... job openings visit HHS USAJobs Home >> NEI for Kids >> Ask a Scientist Video Series Listen All About ...

  11. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... More Information Optical Illusions Printables Ask a Scientist Video Series Why can’t you see colors well ... Why does saltwater sting your eyes? Select a video below to get answers to questions like these ...

  12. Ask a Scientist: What is Color Blindness?

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    Full Text Available ... scientist? Click to Watch Did You Know? An eagle’s eyesight is about five times sharper than a ... you see clearly from five feet away, an eagle can see clearly from 25 feet away. NEI ...

  13. Students as Citizen Scientists - Earth Conservation Corps

    Science.gov (United States)

    This document has an overview of the student workshops on water quality monitoring used to generate citizen scientists. It also includes the main components of the curriculum and contact information for the Earth Conservation Corps to interested parties.

  14. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... Ask a Scientist Video Series Glossary The Visual System Your Eyes’ Natural Defenses Eye Health and Safety ... NEI Website Manager . Department of Health and Human Services | The National Institutes of Health | USA.gov NIH… ...

  15. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... Scientist Video Series Why can’t you see colors well in the dark? Do fish have eyelids? ... video series. Dr. Sheldon Miller answers questions about color blindness, whether it can be treated, and how ...

  16. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... History of the NEI NEI 50th Anniversary NEI Women Scientists Advisory Committee (WSAC) Board of Scientific Counselors ... Emily Y. Chew, M.D., Deputy Clinical Director Education Programs National Eye Health Education Program (NEHEP) Diabetic ...

  17. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... color blindness, whether it can be treated, and how people become color blind. What do my eyes ... Watch What is color blindness? Click to Watch How do I become a scientist? Click to Watch ...

  18. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... Links to More Information Optical Illusions Printables Ask a Scientist Video Series Why can’t you see ... eyelids? Why does saltwater sting your eyes? Select a video below to get answers to questions like ...

  19. 'Lilavati's Daughters: The Women Scientists of India'

    Indian Academy of Sciences (India)

    TSC

    2008-10-31

    biographical essays of about 100 women scientists who have worked and are working in India. The name is drawn from. The Lilavati, a twelfth century treatise in which the mathematician Bhaskaracharya addresses a number of ...

  20. The persistent stereotype: children's images of scientists

    Science.gov (United States)

    Emens McAdam, Janice

    1990-03-01

    Through their reading children learn to regard scientists as eccentrics. It is shown that this stereotype has persisted for over thirty years and affects many adult attitudes. Some methods of breaking the author-reader cycle are suggested.

  1. Strategies for Scientists in Higher Education

    OpenAIRE

    Roche, Joseph

    2016-01-01

    [EN] Scientists have had a role in higher education since the very first institutes of higher education. While this role has evolved considerably in the last century, the period that has seen the most significant changes has been the last four decades. The rapid expansion of the higher education sector and the massification of education through the commitment of the state to free education has seen the role of scientists in higher education in Ireland swell to incorporate new responsibilities...

  2. Comparison of space flight and heavy ion radiation induced genomic/epigenomic mutations in rice (Oryza sativa)

    Science.gov (United States)

    Shi, Jinming; Lu, Weihong; Sun, Yeqing

    2014-04-01

    Rice seeds, after space flight and low dose heavy ion radiation treatment were cultured on ground. Leaves of the mature plants were obtained for examination of genomic/epigenomic mutations by using amplified fragment length polymorphism (AFLP) and methylation sensitive amplification polymorphism (MSAP) method, respectively. The mutation sites were identified by fragment recovery and sequencing. The heritability of the mutations was detected in the next generation. Results showed that both space flight and low dose heavy ion radiation can induce significant alterations on rice genome and epigenome (P < 0.05). For both genetic and epigenetic assays, while there was no significant difference in mutation rates and their ability to be inherited to the next generation, the site of mutations differed between the space flight and radiation treated groups. More than 50% of the mutation sites were shared by two radiation treated groups, radiated with different LET value and dose, while only about 20% of the mutation sites were shared by space flight group and radiation treated group. Moreover, in space flight group, we found that DNA methylation changes were more prone to occur on CNG sequence than CG sequence. Sequencing results proved that both space flight and heavy ion radiation induced mutations were widely spread on rice genome including coding region and repeated region. Our study described and compared the characters of space flight and low dose heavy ion radiation induced genomic/epigenomic mutations. Our data revealed the mechanisms of application of space environment for mutagenesis and crop breeding. Furthermore, this work implicated that the nature of mutations induced under space flight conditions may involve factors beyond ion radiation.

  3. Hereditary kidney cancer syndromes: Genetic disorders driven by alterations in metabolism and epigenome regulation.

    Science.gov (United States)

    Hasumi, Hisashi; Yao, Masahiro

    2018-03-01

    Although hereditary kidney cancer syndrome accounts for approximately five percent of all kidney cancers, the mechanistic insight into tumor development in these rare conditions has provided the foundation for the development of molecular targeting agents currently used for sporadic kidney cancer. In the late 1980s, the comprehensive study for hereditary kidney cancer syndrome was launched in the National Cancer Institute, USA and the first kidney cancer-associated gene, VHL, was identified through kindred analysis of von Hippel-Lindau (VHL) syndrome in 1993. Subsequent molecular studies on VHL function have elucidated that the VHL protein is a component of E3 ubiquitin ligase complex for hypoxia-inducible factor (HIF), which provided the basis for the development of tyrosine kinase inhibitors targeting the HIF-VEGF/PDGF pathway. Recent whole-exome sequencing analysis of sporadic kidney cancer exhibited the recurrent mutations in chromatin remodeling genes and the later study has revealed that several chromatin remodeling genes are altered in kidney cancer kindred at the germline level. To date, more than 10 hereditary kidney cancer syndromes together with each responsible gene have been characterized and most of the causative genes for these genetic disorders are associated with either metabolism or epigenome regulation. In this review article, we describe the molecular mechanisms of how an alteration of each kidney cancer-associated gene leads to renal tumorigenesis as well as denote therapeutic targets elicited by studies on hereditary kidney cancer. © 2018 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

  4. Developmental ethanol exposure impairs locomotor movement in Japanese medaka (Oryzias latipes) larvae targeting epigenome.

    Science.gov (United States)

    Dasmahapatra, Asok K; Carty, Dennis R; Khan, Ikhlas A

    2017-11-01

    Evidence indicated ethanol exposure during development disrupts brain functions that induces fetal alcohol spectrum disorder (FASD) phenotypes with behavioral abnormalities. We aimed to investigate whether prenatal ethanol exposure has any potential impact on behavior of a FASD fish model. Fertilized Japanese medaka (Oryzias latipes) eggs were exposed to 100-300 mM ethanol or 2 mM 5-azacytidine (5-azaC), 0-2 day post fertilization (dpf), in embryo-rearing medium (ERM). Survived embryos were maintained in clean ERM and used either for gene expression analysis on 2- and 6-dpf or allowed to hatch for behavioral study. Photomotor response of 3-4 day post hatch larvae were tracked for 3 h with light-dark transitions. It was observed that larval swimming was phototactic; enhanced in presence of light, declined in dark. Phototactic response was also observed in larvae prenatally exposed to ethanol or 5-azaC; however, the total distance swum by these larvae compared to controls declined. Further analysis indicated that, in light phases, total swimming activity and average swimming speed were reduced in larvae prenatally exposed to ethanol (300 mM) or 5-azaC. Expression analysis of baz1a and baz2a in embryos indicated developmental regulation. Ethanol (100-300 mM) or 5-azaC (2 mM) were able to modulate downregulation of both baz1a and baz2a mRNAs only in 6 dpf embryos of 300 mM ethanol and 5-azaC (2 mM) groups. These studies indicated that prenatal exposure to ethanol or 5-azaC was able to disrupt movements and thus swimming behavior in FASD phenotypes probably due to delayed remodeling of genome and epigenome. Published by Elsevier Ltd.

  5. Comparison of Genomic and Epigenomic Expression in Monozygotic Twins Discordant for Rett Syndrome.

    Directory of Open Access Journals (Sweden)

    Kunio Miyake

    Full Text Available Monozygotic (identical twins have been widely used in genetic studies to determine the relative contributions of heredity and the environment in human diseases. Discordance in disease manifestation between affected monozygotic twins has been attributed to either environmental factors or different patterns of X chromosome inactivation (XCI. However, recent studies have identified genetic and epigenetic differences between monozygotic twins, thereby challenging the accepted experimental model for distinguishing the effects of nature and nurture. Here, we report the genomic and epigenomic sequences in skin fibroblasts of a discordant monozygotic twin pair with Rett syndrome, an X-linked neurodevelopmental disorder characterized by autistic features, epileptic seizures, gait ataxia and stereotypical hand movements. The twins shared the same de novo mutation in exon 4 of the MECP2 gene (G269AfsX288, which was paternal in origin and occurred during spermatogenesis. The XCI patterns in the twins did not differ in lymphocytes, skin fibroblasts, and hair cells (which originate from ectoderm as does neuronal tissue. No reproducible differences were detected between the twins in single nucleotide polymorphisms (SNPs, insertion-deletion polymorphisms (indels, or copy number variations. Differences in DNA methylation between the twins were detected in fibroblasts in the upstream regions of genes involved in brain function and skeletal tissues such as Mohawk Homeobox (MKX, Brain-type Creatine Kinase (CKB, and FYN Tyrosine Kinase Protooncogene (FYN. The level of methylation in these upstream regions was inversely correlated with the level of gene expression. Thus, differences in DNA methylation patterns likely underlie the discordance in Rett phenotypes between the twins.

  6. Stage-specific histone modification profiles reveal global transitions in the Xenopus embryonic epigenome.

    Directory of Open Access Journals (Sweden)

    Tobias D Schneider

    Full Text Available Vertebrate embryos are derived from a transitory pool of pluripotent cells. By the process of embryonic induction, these precursor cells are assigned to specific fates and differentiation programs. Histone post-translational modifications are thought to play a key role in the establishment and maintenance of stable gene expression patterns underlying these processes. While on gene level histone modifications are known to change during differentiation, very little is known about the quantitative fluctuations in bulk histone modifications during development. To investigate this issue we analysed histones isolated from four different developmental stages of Xenopus laevis by mass spectrometry. In toto, we quantified 59 modification states on core histones H3 and H4 from blastula to tadpole stages. During this developmental period, we observed in general an increase in the unmodified states, and a shift from histone modifications associated with transcriptional activity to transcriptionally repressive histone marks. We also compared these naturally occurring patterns with the histone modifications of murine ES cells, detecting large differences in the methylation patterns of histone H3 lysines 27 and 36 between pluripotent ES cells and pluripotent cells from Xenopus blastulae. By combining all detected modification transitions we could cluster their patterns according to their embryonic origin, defining specific histone modification profiles (HMPs for each developmental stage. To our knowledge, this data set represents the first compendium of covalent histone modifications and their quantitative flux during normogenesis in a vertebrate model organism. The HMPs indicate a stepwise maturation of the embryonic epigenome, which may be causal to the progressing restriction of cellular potency during development.

  7. Imprinted genes and transpositions: epigenomic targets for low dose radiation effects. Final report

    International Nuclear Information System (INIS)

    Jirtle, Randy L.

    2012-01-01

    The overall hypothesis of this grant application is that low dose ionizing radiation (LDIR) elicits adaptive responses in part by causing heritable DNA methylation changes in the epigenome. This novel postulate was tested by determining if the level of DNA methylation at the Agouti viable yellow (A vy ) metastable locus is altered, in a dose-dependent manner, by low dose radiation exposure ( vy locus in a sex-specific manner (p=0.004). Average DNA methylation was significantly increased in male offspring exposed to doses between 0.7 cGy and 7.6 cGy with maximum effects at 1.4 cGy and 3.0 cGy (p<0.01). Offspring coat color was concomitantly shifted towards pseudoagouti (p<0.01). Maternal dietary antioxidant supplementation mitigated both the DNA methylation changes and coat color shift in the irradiated offspring (p<0.05). Thus, LDIR exposure during gestation elicits epigenetic alterations that lead to positive adaptive phenotypic changes that are negated with antioxidants, indicating they are mediated in part by oxidative stress. These findings provide evidence that in the isogenic Avy mouse model epigenetic alterations resulting from LDIR play a role in radiation hormesis, bringing into question the assumption that every dose of radiation is harmful. Our findings not only have significant implications concerning the mechanism of hormesis, but they also emphasize the potential importance of this phenomenon in determining human risk at low radiation doses. Since the epigenetic regulation of genes varies markedly between species, the effect of LDIR on other epigenetically labile genes (e.g. imprinted genes) in animals and humans needs to be defined

  8. Epigenomic diversity of colorectal cancer indicated by LINE-1 methylation in a database of 869 tumors

    Directory of Open Access Journals (Sweden)

    Schernhammer Eva S

    2010-05-01

    Full Text Available Abstract Background Genome-wide DNA hypomethylation plays a role in genomic instability and carcinogenesis. LINE-1 (L1 retrotransposon constitutes a substantial portion of the human genome, and LINE-1 methylation correlates with global DNA methylation status. LINE-1 hypomethylation in colon cancer has been strongly associated with poor prognosis. However, whether LINE-1 hypomethylators constitute a distinct cancer subtype remains uncertain. Recent evidence for concordant LINE-1 hypomethylation within synchronous colorectal cancer pairs suggests the presence of a non-stochastic mechanism influencing tumor LINE-1 methylation level. Thus, it is of particular interest to examine whether its wide variation can be attributed to clinical, pathologic or molecular features. Design Utilizing a database of 869 colorectal cancers in two prospective cohort studies, we constructed multivariate linear and logistic regression models for LINE-1 methylation (quantified by Pyrosequencing. Variables included age, sex, body mass index, family history of colorectal cancer, smoking status, tumor location, stage, grade, mucinous component, signet ring cells, tumor infiltrating lymphocytes, CpG island methylator phenotype (CIMP, microsatellite instability, expression of TP53 (p53, CDKN1A (p21, CTNNB1 (β-catenin, PTGS2 (cyclooxygenase-2, and FASN, and mutations in KRAS, BRAF, and PIK3CA. Results Tumoral LINE-1 methylation ranged from 23.1 to 90.3 of 0-100 scale (mean 61.4; median 62.3; standard deviation 9.6, and distributed approximately normally except for extreme hypomethylators [LINE-1 methylation Conclusions LINE-1 extreme hypomethylators appear to constitute a previously-unrecognized, distinct subtype of colorectal cancers, which needs to be confirmed by additional studies. Our tumor LINE-1 methylation data indicate enormous epigenomic diversity of individual colorectal cancers.

  9. How Middle Schoolers Draw Engineers and Scientists

    Science.gov (United States)

    Fralick, Bethany; Kearn, Jennifer; Thompson, Stephen; Lyons, Jed

    2009-02-01

    The perceptions young students have of engineers and scientists are often populated with misconceptions and stereotypes. Although the perceptions that young people have of engineers and of scientists have been investigated separately, they have not been systematically compared. The research reported in this paper explores the question "How are student perceptions of engineers and scientists similar and how are they different?" Approximately 1,600 middle school students from urban and suburban schools in the southeastern United States were asked to draw either an engineer or a scientist at work. Drawings included space for the students to explain what their person was doing in the picture. A checklist to code the drawings was developed and used by two raters. This paper discusses similarities and differences in middle school perceptions of scientists and engineers. Results reveal that the students involved in this study frequently perceive scientists as working indoors conducting experiments. A large fraction of the students have no perception of engineering. Others frequently perceive engineers as working outdoors in manual labor. The findings have implications for the development and implementation of engineering outreach efforts.

  10. Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data.

    Science.gov (United States)

    Kedaigle, Amanda J; Fraenkel, Ernest

    2018-01-01

    With the extraordinary rise in available biological data, biologists and clinicians need unbiased tools for data integration in order to reach accurate, succinct conclusions. Network biology provides one such method for high-throughput data integration, but comes with its own set of algorithmic problems and needed expertise. We provide a step-by-step guide for using Omics Integrator, a software package designed for the integration of transcriptomic, epigenomic, and proteomic data. Omics Integrator can be found at http://fraenkel.mit.edu/omicsintegrator .

  11. Analyzing prospective teachers' images of scientists using positive, negative and stereotypical images of scientists

    Science.gov (United States)

    Subramaniam, Karthigeyan; Esprívalo Harrell, Pamela; Wojnowski, David

    2013-04-01

    Background and purpose : This study details the use of a conceptual framework to analyze prospective teachers' images of scientists to reveal their context-specific conceptions of scientists. The conceptual framework consists of context-specific conceptions related to positive, stereotypical and negative images of scientists as detailed in the literature on the images, role and work of scientists. Sample, design and method : One hundred and ninety-six drawings of scientists, generated by prospective teachers, were analyzed using the Draw-A-Scientist-Test Checklist (DAST-C), a binary linear regression and the conceptual framework. Results : The results of the binary linear regression analysis revealed a statistically significant difference for two DAST-C elements: ethnicity differences with regard to drawing a scientist who was Caucasian and gender differences for indications of danger. Analysis using the conceptual framework helped to categorize the same drawings into positive, stereotypical, negative and composite images of a scientist. Conclusions : The conceptual framework revealed that drawings were focused on the physical appearance of the scientist, and to a lesser extent on the equipment, location and science-related practices that provided the context of a scientist's role and work. Implications for teacher educators include the need to understand that there is a need to provide tools, like the conceptual framework used in this study, to help prospective teachers to confront and engage with their multidimensional perspectives of scientists in light of the current trends on perceiving and valuing scientists. In addition, teacher educators need to use the conceptual framework, which yields qualitative perspectives about drawings, together with the DAST-C, which yields quantitative measure for drawings, to help prospective teachers to gain a holistic outlook on their drawings of scientists.

  12. Nobelist TD LEE Scientist Cooperation Network and Scientist Innovation Ability Model

    OpenAIRE

    Fang, Jin-Qing; Liu, Qiang

    2013-01-01

    Nobelist TD Lee scientist cooperation network (TDLSCN) and their innovation ability are studied. It is found that the TDLSCN not only has the common topological properties both of scale-free and small-world for a general scientist cooperation networks, but also appears the creation multiple-peak phenomenon for number of published paper with year evolution, which become Nobelist TD Lee’s significant mark distinguished from other scientists. This new phenomenon has not been revealed in the scie...

  13. Assessing scientists for hiring, promotion, and tenure

    Science.gov (United States)

    Naudet, Florian; Cristea, Ioana A.; Miedema, Frank; Ioannidis, John P. A.; Goodman, Steven N.

    2018-01-01

    Assessment of researchers is necessary for decisions of hiring, promotion, and tenure. A burgeoning number of scientific leaders believe the current system of faculty incentives and rewards is misaligned with the needs of society and disconnected from the evidence about the causes of the reproducibility crisis and suboptimal quality of the scientific publication record. To address this issue, particularly for the clinical and life sciences, we convened a 22-member expert panel workshop in Washington, DC, in January 2017. Twenty-two academic leaders, funders, and scientists participated in the meeting. As background for the meeting, we completed a selective literature review of 22 key documents critiquing the current incentive system. From each document, we extracted how the authors perceived the problems of assessing science and scientists, the unintended consequences of maintaining the status quo for assessing scientists, and details of their proposed solutions. The resulting table was used as a seed for participant discussion. This resulted in six principles for assessing scientists and associated research and policy implications. We hope the content of this paper will serve as a basis for establishing best practices and redesigning the current approaches to assessing scientists by the many players involved in that process. PMID:29596415

  14. Assessing scientists for hiring, promotion, and tenure.

    Science.gov (United States)

    Moher, David; Naudet, Florian; Cristea, Ioana A; Miedema, Frank; Ioannidis, John P A; Goodman, Steven N

    2018-03-01

    Assessment of researchers is necessary for decisions of hiring, promotion, and tenure. A burgeoning number of scientific leaders believe the current system of faculty incentives and rewards is misaligned with the needs of society and disconnected from the evidence about the causes of the reproducibility crisis and suboptimal quality of the scientific publication record. To address this issue, particularly for the clinical and life sciences, we convened a 22-member expert panel workshop in Washington, DC, in January 2017. Twenty-two academic leaders, funders, and scientists participated in the meeting. As background for the meeting, we completed a selective literature review of 22 key documents critiquing the current incentive system. From each document, we extracted how the authors perceived the problems of assessing science and scientists, the unintended consequences of maintaining the status quo for assessing scientists, and details of their proposed solutions. The resulting table was used as a seed for participant discussion. This resulted in six principles for assessing scientists and associated research and policy implications. We hope the content of this paper will serve as a basis for establishing best practices and redesigning the current approaches to assessing scientists by the many players involved in that process.

  15. Seismic maps foster landmark legislation

    Science.gov (United States)

    Borcherdt, Roger D.; Brown, Robert B.; Page, Robert A.; Wentworth, Carl M.; Hendley, James W.

    1995-01-01

    When a powerful earthquake strikes an urban region, damage concentrates not only near the quake's source. Damage can also occur many miles from the source in areas of soft ground. In recent years, scientists have developed ways to identify and map these areas of high seismic hazard. This advance has spurred pioneering legislation to reduce earthquake losses in areas of greatest hazard.

  16. Transcriptome Characterization by RNA-seq Unravels the Mechanisms of Butyrate-Induced Epigenomic Regulation in Bovine Cells

    Science.gov (United States)

    Wu, Sitao; Li, Robert W.; Li, Weizhong; Li, Cong-jun

    2012-01-01

    Short-chain fatty acids (SCFAs), especially butyrate, affect cell differentiation, proliferation, and motility. Butyrate also induces cell cycle arrest and apoptosis through its inhibition of histone deacetylases (HDACs). In addition, butyrate is a potent inducer of histone hyper-acetylation in cells. Therefore, this SCFA provides an excellent in vitro model for studying the epigenomic regulation of gene expression induced by histone acetylation. In this study, we analyzed the differential in vitro expression of genes induced by butyrate in bovine epithelial cells by using deep RNA-sequencing technology (RNA-seq). The number of sequences read, ranging from 57,303,693 to 78,933,744, were generated per sample. Approximately 11,408 genes were significantly impacted by butyrate, with a false discovery rate (FDR) butyrate included cell morphological changes, cell cycle arrest, and apoptosis. Our results provided insight into the transcriptome alterations induced by butyrate, which will undoubtedly facilitate our understanding of the molecular mechanisms underlying butyrate-induced epigenomic regulation in bovine cells. PMID:22615851

  17. Transcriptome characterization by RNA-seq unravels the mechanisms of butyrate-induced epigenomic regulation in bovine cells.

    Directory of Open Access Journals (Sweden)

    Sitao Wu

    Full Text Available Short-chain fatty acids (SCFAs, especially butyrate, affect cell differentiation, proliferation, and motility. Butyrate also induces cell cycle arrest and apoptosis through its inhibition of histone deacetylases (HDACs. In addition, butyrate is a potent inducer of histone hyper-acetylation in cells. Therefore, this SCFA provides an excellent in vitro model for studying the epigenomic regulation of gene expression induced by histone acetylation. In this study, we analyzed the differential in vitro expression of genes induced by butyrate in bovine epithelial cells by using deep RNA-sequencing technology (RNA-seq. The number of sequences read, ranging from 57,303,693 to 78,933,744, were generated per sample. Approximately 11,408 genes were significantly impacted by butyrate, with a false discovery rate (FDR <0.05. The predominant cellular processes affected by butyrate included cell morphological changes, cell cycle arrest, and apoptosis. Our results provided insight into the transcriptome alterations induced by butyrate, which will undoubtedly facilitate our understanding of the molecular mechanisms underlying butyrate-induced epigenomic regulation in bovine cells.

  18. Impact of body size, nutrition and socioeconomic position in early life on the epigenome: a systematic review protocol.

    Science.gov (United States)

    Maddock, Jane; Wulaningsih, Wahyu; Hardy, Rebecca

    2017-07-05

    Body size, nutrition and socioeconomic position (SEP) in early life have been associated with a range of later life health outcomes. Epigenetic regulation is one mechanism through which these early life factors may impact later life health. The aim of this review protocol is to outline procedures to document the influence of body size, nutrition and SEP in early life on the epigenome. MEDLINE, Embase and BIOSIS will be systematically searched using pre-defined keywords. Additional studies will be identified through manual searching of reference lists. Two independent researchers will assess the eligibility and quality of each study, with disagreements being resolved through discussion or a third reviewer. Studies will be included if they have epigenetic markers measured either at the same time as, or after, the early life exposure and, have a measure of body size, nutrition or SEP in early life (up to 12 years), are in the English language and are from a sample of community-dwelling participants. This protocol will be used to collate the evidence for the effect of early life factors on the epigenome. Findings will form a component of a wider research study examining epigenetic responses to exposures in early life and over the life course and its impact on healthy ageing using data from population-based cohort studies. PROSPERO CRD42016050193.

  19. Context-Specific Effects of TGF-β/SMAD3 in Cancer Are Modulated by the Epigenome.

    Science.gov (United States)

    Tufegdzic Vidakovic, Ana; Rueda, Oscar M; Vervoort, Stephin J; Sati Batra, Ankita; Goldgraben, Mae Akilina; Uribe-Lewis, Santiago; Greenwood, Wendy; Coffer, Paul J; Bruna, Alejandra; Caldas, Carlos

    2015-12-22

    The transforming growth factor beta (TGF-β) signaling pathway exerts opposing effects on cancer cells, acting as either a tumor promoter or a tumor suppressor. Here, we show that these opposing effects are a result of the synergy between SMAD3, a downstream effector of TGF-β signaling, and the distinct epigenomes of breast-tumor-initiating cells (BTICs). These effects of TGF-β are associated with distinct gene expression programs, but genomic SMAD3 binding patterns are highly similar in the BTIC-promoting and BTIC-suppressing contexts. Our data show cell-type-specific patterns of DNA and histone modifications provide a modulatory layer by determining accessibility of genes to regulation by TGF-β/SMAD3. LBH, one such context-specific target gene, is regulated according to its DNA methylation status and is crucial for TGF-β-dependent promotion of BTICs. Overall, these results reveal that the epigenome plays a central and previously overlooked role in shaping the context-specific effects of TGF-β in cancer. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  20. An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression.

    Science.gov (United States)

    Qin, Yufeng; Roberts, John D; Grimm, Sara A; Lih, Fred B; Deterding, Leesa J; Li, Ruifang; Chrysovergis, Kaliopi; Wade, Paul A

    2018-01-23

    The gut microbiome, a key constituent of the colonic environment, has been implicated as an important modulator of human health. The eukaryotic epigenome is postulated to respond to environmental stimuli through alterations in chromatin features and, ultimately, gene expression. How the host mediates epigenomic responses to gut microbiota is an emerging area of interest. Here, we profile the gut microbiome and chromatin characteristics in colon epithelium from mice fed either an obesogenic or control diet, followed by an analysis of the resultant changes in gene expression. The obesogenic diet shapes the microbiome prior to the development of obesity, leading to altered bacterial metabolite production which predisposes the host to obesity. This microbiota-diet interaction leads to changes in histone modification at active enhancers that are enriched for binding sites for signal responsive transcription factors. These alterations of histone methylation and acetylation are associated with signaling pathways integral to the development of colon cancer. The transplantation of obesogenic diet-conditioned microbiota into germ free mice, combined with an obesogenic diet, recapitulates the features of the long-term diet regimen. The diet/microbiome-dependent changes are reflected in both the composition of the recipient animals' microbiome as well as in the set of transcription factor motifs identified at diet-influenced enhancers. These findings suggest that the gut microbiome, under specific dietary exposures, stimulates a reprogramming of the enhancer landscape in the colon, with downstream effects on transcription factors. These chromatin changes may be associated with those seen during colon cancer development.

  1. Alcohol effects on the epigenome in the germline: Role in the inheritance of alcohol-related pathology.

    Science.gov (United States)

    Chastain, Lucy G; Sarkar, Dipak K

    2017-05-01

    Excessive alcohol exposure has severe health consequences, and clinical and animal studies have demonstrated that disruptions in the epigenome of somatic cells, such as those in brain, are an important factor in the development of alcohol-related pathologies, such as alcohol-use disorders (AUDs) and fetal alcohol spectrum disorders (FASDs). It is also well known that alcohol-related health problems are passed down across generations in human populations, but the complete mechanisms for this phenomenon are currently unknown. Recent studies in animal models have suggested that epigenetic factors are also responsible for the transmission of alcohol-related pathologies across generations. Alcohol exposure has been shown to induce changes in the epigenome of sperm of exposed male animals, and these epimutations are inherited in the offspring. This paper reviews evidence for multigenerational and transgenerational epigenetic inheritance of alcohol-related pathology through the germline. We also review the literature on the epigenetic effects of alcohol exposure on somatic cells in brain, and its contribution to AUDs and FASDs. We note gaps in knowledge in this field, such as the lack of clinical studies in human populations and the lack of data on epigenetic inheritance via the female germline, and we suggest future research directions. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Legal education for scientists at Fall Meeting

    Science.gov (United States)

    Uhlenbrock, Kristan

    2012-10-01

    In today's increasingly polarized political climate, science is becoming more politicized, which in turn leads to scientists facing an increased involvement in legal discussion about their work, their correspondence, and their public statements. At times these attacks on scientists and their academic freedom are unwarranted and can leave many confused and wondering how to handle the situation. To help out, AGU and the Climate Science Legal Defense Fund (CSLDF) have partnered to prepare the scientific community for these challenges through a Legal Education Series, a series of webinars along with events at AGU's 2012 Fall Meeting. This series provides scientists with information to help guide and update them on legal issues and situations currently making their way through the courts.

  3. Women scientists joining Rokkasho women to sciences

    Energy Technology Data Exchange (ETDEWEB)

    Aratani, Michi [Office of Regional Collaboration, Institute for Environmental Sciences, Rokkasho, Aomori (Japan); Sasagawa, Sumiko

    1999-09-01

    Women scientists generally play a great role in the public acceptance (PA) for the national policy of atomic energy developing in Japan. The reason may be that, when a woman scientist stands in the presence of women audience, she will be ready to be accepted by them as a person with the same gender, emotion and thought to themselves. A case of interchange between the Rokkasho women and the women scientists either resident at the nuclear site of Rokkasho or staying for a short time at Rokkasho by invitation has been described from the viewpoint of PA for the national policy of atomic energy developing, and more fundamentally, for promotion of science education. (author)

  4. Women scientists joining Rokkasho women to sciences

    International Nuclear Information System (INIS)

    Aratani, Michi; Sasagawa, Sumiko

    1999-01-01

    Women scientists generally play a great role in the public acceptance (PA) for the national policy of atomic energy developing in Japan. The reason may be that, when a woman scientist stands in the presence of women audience, she will be ready to be accepted by them as a person with the same gender, emotion and thought to themselves. A case of interchange between the Rokkasho women and the women scientists either resident at the nuclear site of Rokkasho or staying for a short time at Rokkasho by invitation has been described from the viewpoint of PA for the national policy of atomic energy developing, and more fundamentally, for promotion of science education. (author)

  5. Scientists warn DOE of dwindling funding

    International Nuclear Information System (INIS)

    Anon.

    1994-01-01

    Fusion scientists have raised their voices to let the Department of Energy know that they are concerned about the DOE's commitment to fusion research. In a letter dated February 28, 1994, 37 scientists from 21 institutions noted that open-quotes US funding for fusion has steadily decreased: It is now roughly half its level of 1980. This peculiar and painful circumstance has forced the program to contract drastically, losing skilled technical personnel, even as it faces its most exciting opportunities.close quotes The letter was addressed to Martha Krebs, the DOE's director of the Office of Energy Research, and N. Anne Davies, associated director for fusion energy. The scientists wanted to make two points. The first was that fusion energy research, only midway between concept and commercialization, deserves major reinvestment. The second was that basic scientific knowledge in the area of fusion, not just applied engineering, must remain a priority

  6. A distant light scientists and public policy

    CERN Document Server

    2000-01-01

    A collection of essays by a Nobel Prize Laureate on a wide range of critical issues facing the world, and the role of scientists in solving these problems. Kendall has been closely involved with the Union of Concerned Scientists, a group that began as an informal assocation at MIT in 1969 to protest US involvement in Vietnam and is today an organization with an annual budget exceeding $6 million, with 100,000 supporters worldwide. UCD is today a voice of authority in US government science policy, particularly with regard to environment issues, most recently the worldwide initiatives on global warming. Together, these essays represent both the sucessses and failures of science to impact public policy, the challenges facing scientists, and offers practical guidelines for involvement in science policy. The essays are roughly chronological, organized by subject with introductions, beginning with the controversies on nuclear power safety and Three Mile Island,then followed by sections on national security issues, ...

  7. The Normative Orientations of Climate Scientists.

    Science.gov (United States)

    Bray, Dennis; von Storch, Hans

    2017-10-01

    In 1942 Robert K. Merton tried to demonstrate the structure of the normative system of science by specifying the norms that characterized it. The norms were assigned the abbreviation CUDOs: Communism, Universalism, Disinterestedness, and Organized skepticism. Using the results of an on-line survey of climate scientists concerning the norms of science, this paper explores the climate scientists' subscription to these norms. The data suggests that while Merton's CUDOs remain the overall guiding moral principles, they are not fully endorsed or present in the conduct of climate scientists: there is a tendency to withhold results until publication, there is the intention of maintaining property rights, there is external influence defining research and the tendency to assign the significance of authored work according to the status of the author rather than content of the paper. These are contrary to the norms of science as proposed by Robert K. Merton.

  8. Phobias and underutilization of university scientists

    International Nuclear Information System (INIS)

    Mandra, Y.T.

    1992-01-01

    This paper reports that there is an urgent need for a large scale, nationwide education program designed to correct the almost ubiquitous misconceptions that exist because of the public's misinformation about commercial nuclear power. It is suggested that this program use only university professors and that it have a precisely defined target of community colleges. To do this a Distinguished Visiting Scientist Program needs to be established by the Department of Energy. This would be the means by which these visiting scientists could get invited for 2-day visits at community colleges. When on campus the visiting scientist would give lectures in the morning and it the afternoon to student and professors on just two topics dealing with commercial nuclear power: nuclear plants and disposal of the waste. It is suggested that a pilot program be done in California and selected hub-centers, and that it be evaluated by an independent agency so that it can be improved

  9. Science communication a practical guide for scientists

    CERN Document Server

    Bowater, Laura

    2012-01-01

    Science communication is a rapidly expanding area and meaningful engagement between scientists and the public requires effective communication. Designed to help the novice scientist get started with science communication, this unique guide begins with a short history of science communication before discussing the design and delivery of an effective engagement event. Along with numerous case studies written by highly regarded international contributors, the book discusses how to approach face-to-face science communication and engagement activities with the public while providing tips to avoid potential pitfalls. This book has been written for scientists at all stages of their career, including undergraduates and postgraduates wishing to engage with effective science communication for the first time, or looking to develop their science communication portfolio.

  10. Advice to young behavioral and cognitive scientists.

    Science.gov (United States)

    Weisman, Ronald G

    2008-02-01

    Modeled on Medawar's Advice to a Young Scientist [Medawar, P.B., 1979. Advice to a Young Scientist. Basic Books, New York], this article provides advice to behavioral and cognitive scientists. An important guiding principle is that the study of comparative cognition and behavior are natural sciences tasked with explaining nature. The author advises young scientists to begin with a natural phenomenon and then bring it into the laboratory, rather than beginning in the laboratory and hoping for an application in nature. He suggests collaboration as a way to include research outside the scientist's normal competence. He then discusses several guides to good science. These guides include Tinbergen's [Tinbergen, N., 1963. On aims and methods of ethology. Zeitschrift für Tierpsychologie, 20, 410-433. This journal was renamed Ethology in 1986. Also reprinted in Anim. Biol. 55, 297-321, 2005] four "why" questions, Platt's [Platt, J.R., 1964. Strong inference. Science 146, 347-353, (http://weber.ucsd.edu/~jmoore/courses/Platt1964.pdf)] notion of strong inference using multiple alternative hypotheses, and the idea that positive controls help scientists to follow Popper's [Popper, K.R., 1959. The Logic of Scientific Discovery. Basic Books, New York, p. 41] advice about disproving hypotheses. The author also recommends Strunk and White's [Strunk, W., White, E.B., 1979. The Elements of Style, third ed. Macmillan, New York] rules for sound writing, and he provides his personal advice on how to use the anticipation of peer review to improve research and how to decode editors' and reviewers' comments about submitted articles.

  11. The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until Infection

    Science.gov (United States)

    Freitag, Michael; Parrinello, Hugues; Groth, Marco; Emans, Rémi; Cosseau, Céline; Grunau, Christoph

    2015-01-01

    Background Chromatin structure can control gene expression and can define specific transcription states. For example, bivalent methylation of histone H3K4 and H3K27 is linked to poised transcription in vertebrate embryonic stem cells (ESC). It allows them to rapidly engage specific developmental pathways. We reasoned that non-vertebrate metazoans that encounter a similar developmental constraint (i.e. to quickly start development into a new phenotype) might use a similar system. Schistosomes are parasitic platyhelminthes that are characterized by passage through two hosts: a mollusk as intermediate host and humans or rodents as definitive host. During its development, the parasite undergoes drastic changes, most notable immediately after infection of the definitive host, i.e. during the transition from the free-swimming cercariae into adult worms. Methodology/Principal Findings We used Chromatin Immunoprecipitation followed by massive parallel sequencing (ChIP-Seq) to analyze genome-wide chromatin structure of S. mansoni on the level of histone modifications (H3K4me3, H3K27me3, H3K9me3, and H3K9ac) in cercariae, schistosomula and adults (available at http://genome.univ-perp.fr). We saw striking differences in chromatin structure between the developmental stages, but most importantly we found that cercariae possess a specific combination of marks at the transcription start sites (TSS) that has similarities to a structure found in ESC. We demonstrate that in cercariae no transcription occurs, and we provide evidences that cercariae do not possess large numbers of canonical stem cells. Conclusions/Significance We describe here a broad view on the epigenome of a metazoan parasite. Most notably, we find bivalent histone H3 methylation in cercariae. Methylation of H3K27 is removed during transformation into schistosomula (and stays absent in adults) and transcription is activated. In addition, shifts of H3K9 methylation and acetylation occur towards upstream and

  12. The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until Infection.

    Directory of Open Access Journals (Sweden)

    David Roquis

    Full Text Available Chromatin structure can control gene expression and can define specific transcription states. For example, bivalent methylation of histone H3K4 and H3K27 is linked to poised transcription in vertebrate embryonic stem cells (ESC. It allows them to rapidly engage specific developmental pathways. We reasoned that non-vertebrate metazoans that encounter a similar developmental constraint (i.e. to quickly start development into a new phenotype might use a similar system. Schistosomes are parasitic platyhelminthes that are characterized by passage through two hosts: a mollusk as intermediate host and humans or rodents as definitive host. During its development, the parasite undergoes drastic changes, most notable immediately after infection of the definitive host, i.e. during the transition from the free-swimming cercariae into adult worms.We used Chromatin Immunoprecipitation followed by massive parallel sequencing (ChIP-Seq to analyze genome-wide chromatin structure of S. mansoni on the level of histone modifications (H3K4me3, H3K27me3, H3K9me3, and H3K9ac in cercariae, schistosomula and adults (available at http://genome.univ-perp.fr. We saw striking differences in chromatin structure between the developmental stages, but most importantly we found that cercariae possess a specific combination of marks at the transcription start sites (TSS that has similarities to a structure found in ESC. We demonstrate that in cercariae no transcription occurs, and we provide evidences that cercariae do not possess large numbers of canonical stem cells.We describe here a broad view on the epigenome of a metazoan parasite. Most notably, we find bivalent histone H3 methylation in cercariae. Methylation of H3K27 is removed during transformation into schistosomula (and stays absent in adults and transcription is activated. In addition, shifts of H3K9 methylation and acetylation occur towards upstream and downstream of the transcriptional start site (TSS. We conclude

  13. Imprinted genes and transpositions: epigenomic targets for low dose radiation effects. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Jirtle, Randy L.

    2012-10-11

    The overall hypothesis of this grant application is that low dose ionizing radiation (LDIR) elicits adaptive responses in part by causing heritable DNA methylation changes in the epigenome. This novel postulate was tested by determining if the level of DNA methylation at the Agouti viable yellow (A{sup vy}) metastable locus is altered, in a dose-dependent manner, by low dose radiation exposure (<10 cGy) during early gestation. This information is particularly important to ascertain given the increased use of CT scans in disease diagnosis, increased number of people predicted to live and work in space, and the present concern about radiological terrorism. We showed for the first time that LDIR significantly increased DNA methylation at the A{sup vy} locus in a sex-specific manner (p=0.004). Average DNA methylation was significantly increased in male offspring exposed to doses between 0.7 cGy and 7.6 cGy with maximum effects at 1.4 cGy and 3.0 cGy (p<0.01). Offspring coat color was concomitantly shifted towards pseudoagouti (p<0.01). Maternal dietary antioxidant supplementation mitigated both the DNA methylation changes and coat color shift in the irradiated offspring (p<0.05). Thus, LDIR exposure during gestation elicits epigenetic alterations that lead to positive adaptive phenotypic changes that are negated with antioxidants, indicating they are mediated in part by oxidative stress. These findings provide evidence that in the isogenic Avy mouse model epigenetic alterations resulting from LDIR play a role in radiation hormesis, bringing into question the assumption that every dose of radiation is harmful. Our findings not only have significant implications concerning the mechanism of hormesis, but they also emphasize the potential importance of this phenomenon in determining human risk at low radiation doses. Since the epigenetic regulation of genes varies markedly between species, the effect of LDIR on other epigenetically labile genes (e.g. imprinted genes) in

  14. Media and the making of scientists

    Science.gov (United States)

    O'Keeffe, Moira

    This dissertation explores how scientists and science students respond to fictional, visual media about science. I consider how scientists think about images of science in relation to their own career paths from childhood onwards. I am especially interested in the possibility that entertainment media can inspire young people to learn about science. Such inspiration is badly needed, as schools are failing to provide it. Science education in the United States is in a state of crisis. Studies repeatedly find low levels of science literacy in the U.S. This bleak situation exists during a boom in the popularity of science-oriented television shows and science fiction movies. How might entertainment media play a role in helping young people engage with science? To grapple with these questions, I interviewed a total of fifty scientists and students interested in science careers, representing a variety of scientific fields and demographic backgrounds, and with varying levels of interest in science fiction. Most respondents described becoming attracted to the sciences at a young age, and many were able to identify specific sources for this interest. The fact that interest in the sciences begins early in life, demonstrates a potentially important role for fictional media in the process of inspiration, perhaps especially for children without access to real-life scientists. One key aspect to the appeal of fiction about science is how scientists are portrayed as characters. Scientists from groups traditionally under-represented in the sciences often sought out fictional characters with whom they could identify, and viewers from all backgrounds preferred well-rounded characters to the extreme stereotypes of mad or dorky scientists. Genre is another aspect of appeal. Some respondents identified a specific role for science fiction: conveying a sense of wonder. Visual media introduce viewers to the beauty of science. Special effects, in particular, allow viewers to explore the

  15. Career Management for Scientists and Engineers

    Science.gov (United States)

    Borchardt, John K.

    2000-05-01

    This book will be an important resource for both new graduates and mid-career scientists, engineers, and technicians. Through taking stock of existing or desired skills and goals, it provides both general advice and concrete examples to help asses a current job situation or prospect, and to effectively pursue and attain new ones. Many examples of properly adapted resumes and interview techniques, as well as plenty of practical advice about adaptation to new workplace cultural paradigms, such as team-based management, make this book an invaluable reference for the professional scientist in today's volatile job market.

  16. Italian weather scientists and sports scientists – is there a link?

    African Journals Online (AJOL)

    The scientists were sentenced to 6 years' imprisonment for giving. 'inexact, incomplete and contradictory information' about whether small tremors felt in the weeks and months before the earthquake constituted grounds for a ... Although the scientists claimed that the science of tremors was not ... The list goes on and on.

  17. How to Grow Project Scientists: A Systematic Approach to Developing Project Scientists

    Science.gov (United States)

    Kea, Howard

    2011-01-01

    The Project Manager is one of the key individuals that can determine the success or failure of a project. NASA is fully committed to the training and development of Project Managers across the agency to ensure that highly capable individuals are equipped with the competencies and experience to successfully lead a project. An equally critical position is that of the Project Scientist. The Project Scientist provides the scientific leadership necessary for the scientific success of a project by insuring that the mission meets or exceeds the scientific requirements. Traditionally, NASA Goddard project scientists were appointed and approved by the Center Science Director based on their knowledge, experience, and other qualifications. However the process to obtain the necessary knowledge, skills and abilities was not documented or done in a systematic way. NASA Goddard's current Science Director, Nicholas White saw the need to create a pipeline for developing new projects scientists, and appointed a team to develop a process for training potential project scientists. The team members were Dr. Harley Thronson, Chair, Dr. Howard Kea, Mr. Mark Goldman, DACUM facilitator and the late Dr. Michael VanSteenberg. The DACUM process, an occupational analysis and evaluation system, was used to produce a picture of the project scientist's duties, tasks, knowledge, and skills. The output resulted in a 3-Day introductory course detailing all the required knowledge, skills and abilities a scientist must develop over time to be qualified for selections as a Project Scientist.

  18. Forensic scientists' conclusions: how readable are they for non-scientist report-users?

    Science.gov (United States)

    Howes, Loene M; Kirkbride, K Paul; Kelty, Sally F; Julian, Roberta; Kemp, Nenagh

    2013-09-10

    Scientists have an ethical responsibility to assist non-scientists to understand their findings and expert opinions before they are used as decision-aids within the criminal justice system. The communication of scientific expert opinion to non-scientist audiences (e.g., police, lawyers, and judges) through expert reports is an important but under-researched issue. Readability statistics were used to assess 111 conclusions from a proficiency test in forensic glass analysis. The conclusions were written using an average of 23 words per sentence, and approximately half of the conclusions were expressed using the active voice. At an average Flesch-Kincaid Grade level of university undergraduate (Grade 13), and Flesch Reading Ease score of difficult (42), the conclusions were written at a level suitable for people with some tertiary education in science, suggesting that the intended non-scientist readers would find them difficult to read. To further analyse the readability of conclusions, descriptive features of text were used: text structure; sentence structure; vocabulary; elaboration; and coherence and unity. Descriptive analysis supported the finding that texts were written at a level difficult for non-scientists to read. Specific aspects of conclusions that may pose difficulties for non-scientists were located. Suggestions are included to assist scientists to write conclusions with increased readability for non-scientist readers, while retaining scientific integrity. In the next stage of research, the readability of expert reports in their entirety is to be explored. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  19. Scientists' coping strategies in an evolving research system: the case of life scientists in the UK

    NARCIS (Netherlands)

    Morris, Norma; Rip, Arie

    2006-01-01

    Scientists in academia have struggled to adjust to a policy climate of uncertain funding and loss of freedom from direction and control. How UK life scientists have negotiated this challenge, and with what consequences for their research and the research system, is the empirical entrance point of

  20. The Genome Health Clinic and Genome Health Nutrigenomics concepts: diagnosis and nutritional treatment of genome and epigenome damage on an individual basis.

    Science.gov (United States)

    Fenech, Michael

    2005-07-01

    The evidence of a direct link between increased genome/epigenome damage and elevated risk for adverse health outcomes during the various stages of life, such as infertility, foetal development and cancer is becoming increasingly stronger. The latter is briefly reviewed against a background of evidence indicating that genome and epigenome damage biomarkers, in the absence of overt exposure of genotoxins, are themselves sensitive indicators of deficiency in micronutrients required as cofactors or as components of DNA repair enzymes, for maintenance methylation of CpG sequences and prevention of DNA oxidation and/or uracil incorporation into DNA. The latter is illustrated with cross-sectional and dietary intervention data obtained using the micronucleus assay and other efficient biomarkers for diagnosing genome and/or epigenome instability. The concept of recommended dietary allowances for genome stability and how this could be achieved is discussed. The 'Genome Health Nutrigenomics' concept is also introduced to define and focus attention on the specialized research area of how diet impacts on genome stability and how genotype determines nutritional requirements for genome health maintenance. The review concludes with a vision for a paradigm shift in disease prevention strategy based on the diagnosis and nutritional treatment of genome/epigenome damage on an individual basis, i.e. The Genome Health Clinic.

  1. An epigenome-wide study of obesity in African American youth and young adults : novel findings, replication in neutrophils, and relationship with gene expression

    NARCIS (Netherlands)

    Wang, Xiaoling; Pan, Yue; Zhu, Haidong; Hao, Guang; Huang, Yisong; Barnes, Vernon; Shi, Huidong; Snieder, Harold; Pankow, James; North, Kari; Grove, Megan; Guan, Weihua; Demerath, Ellen; Dong, Yanbin; Su, Shaoyong

    2018-01-01

    Background: We conducted an epigenome-wide association study (EWAS) on obesity in healthy youth and young adults and further examined to what extent identified signals influenced gene expression and were independent of cell type composition and obesity-related cardio-metabolic risk factors.

  2. The Oratorical Scientist: A Guide for Speechcraft and Presentation for Scientists

    Science.gov (United States)

    Lau, G. E.

    2015-12-01

    Public speaking organizations are highly valuable for individuals seeking to improve their skills in speech development and delivery. The methodology of such groups usually focuses on repetitive, guided practice. Toastmasters International, for instance, uses a curriculum based on topical manuals that guide their members through some number of prepared speeches with specific goals for each speech. I have similarly developed a public speaking manual for scientists with the intention of guiding scientists through the development and presentation of speeches that will help them hone their abilities as public speakers. I call this guide The Oratorical Scientist. The Oratorical Scientist will be a free, digital publication that is meant to guide scientists through five specific types of speech that the scientist may be called upon to deliver during their career. These five speeches are: The Coffee Talk, The Educational Talk, Research Talks for General Science Audiences, Research Talks for Specific Subdiscipline Audiences, and Taking the Big Stage (talks for public engagement). Each section of the manual focuses on speech development, rehearsal, and presentation for each of these specific types of speech. The curriculum was developed primarily from my personal experiences in public engagement. Individuals who use the manual may deliver their prepared speeches to groups of their peers (e.g. within their research group) or through video sharing websites like Youtube and Vimeo. Speeches that are broadcast online can then be followed and shared through social media networks (e.g. #OratoricalScientist), allowing a larger audience to evaluate the speech and to provide criticism. I will present The Oratorical Scientist, a guide for scientists to become better public speakers. The process of guided repetitive practice of scientific talks will improve the speaking capabilities of scientists, in turn benefitting science communication and public engagement.

  3. Educational Mismatch and the Careers of Scientists

    Science.gov (United States)

    Bender, Keith A.; Heywood, John S.

    2011-01-01

    Previous research confirms that many employees work in jobs not well matched to their skills and education, resulting in lower pay and job satisfaction. While this literature typically uses cross-sectional data, we examine the evolution of mismatch and its consequences over a career, by using a panel data set of scientists in the USA. The results…

  4. Alexandre Gustave Eiffel: An Engineer Scientist

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 9. Alexandre Gustave Eiffel: An Engineer Scientist. Ananth Ramaswamy. General Article Volume 14 Issue 9 September 2009 pp 840-848. Fulltext. Click here to view fulltext PDF. Permanent link:

  5. Scientists riff on fabric of the universe

    CERN Multimedia

    2008-01-01

    Their music may be the scourge of parents, but the thrashing guitars of heavy metal bands like Metallica and Iron Maiden could help explain the mysteries of the universe. The string vibrations from the frantic strumming of rock guitarists form the basis of String Theory, a mathematic theory that seeks to explain what the world is made of, says scientist Mark Lewney.

  6. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... Accomplishments Budget and Congress About the NEI Director History of the NEI NEI 50th Anniversary NEI Women Scientists ... sight, and the special health problems and requirements of the blind.” News & Events ... bios Statistics and Data Resources for the media Pressroom Contacts ...

  7. GI Taylor–An Amateur Scientist

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 10. G. I. Taylor – An Amateur Scientist. Jaywant H Arakeri. Article-in-a-Box Volume 9 Issue 10 October 2004 pp 3-5. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/009/10/0003-0005 ...

  8. Non-natives: 141 scientists object

    NARCIS (Netherlands)

    Simberloff, D.; Van der Putten, W.H.

    2011-01-01

    Supplementary information to: Non-natives: 141 scientists object Full list of co-signatories to a Correspondence published in Nature 475, 36 (2011); doi: 10.1038/475036a. Daniel Simberloff University of Tennessee, Knoxville, Tennessee, USA. dsimberloff@utk.edu Jake Alexander Institute of Integrative

  9. Challenges before Women Scientists, Technologists & Engineers

    Indian Academy of Sciences (India)

    Social Responsibility. Panel Discussion/Round. Table Session. Group of eminent women scientists, Engineers, Technologists, Administrators,. Social workers ... Red and laterite soils are found here which are quite rich in minerals. The area near Rourkela is rich in iron-ore hence a steel plant is situated in Rourkela.

  10. Scientist Researches Way to Reduce Global Warming

    Science.gov (United States)

    For the last four years, scientists at the USDA, Agricultural Research Service, Northern Plains Agricultural Research Laboratory have been searching for alternative soil and crop management practices to reduce greenhouse gas emissions and increase carbon and nitrogen sequestration. “If we can redu...

  11. Alexandre Gustave Eiffel: An Engineer Scientist

    Indian Academy of Sciences (India)

    ... Journals; Resonance – Journal of Science Education; Volume 14; Issue 9. Alexandre Gustave Eiffel: An Engineer Scientist. Ananth Ramaswamy. General Article Volume 14 Issue 9 September ... Author Affiliations. Ananth Ramaswamy1. Civil Engineering Department, Indian Institute of Science, Bangalore 560 012, India.

  12. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... Search the NEI Website search NEI on Social Media | Search A-Z | en español | Text size S M L About NEI NEI Research Accomplishments Budget and Congress About the NEI Director History of the NEI NEI 50th Anniversary NEI Women Scientists Advisory Committee (WSAC) Board of Scientific Counselors ...

  13. The Political Scientist as Local Campaign Consultant

    Science.gov (United States)

    Crew, Robert E., Jr.

    2011-01-01

    During my 45 years as an academic, I have followed the admonition sometimes attributed to the legendary Jedi warrior Obi-Wan Kenobe that political scientists should "use [their] power for good and not for evil." In this spirit, I have devoted substantial portions of my career to public service by providing strategic advice and campaign management…

  14. A Systematic Identification of Scientists on Twitter

    Energy Technology Data Exchange (ETDEWEB)

    Ke, Q.; Ahn, Y.Y.; Sugimoto, C.R.

    2016-07-01

    There is an increasing use of Twitter and other social media to estimate the broader social impacts of scholarship. However, without systematic understanding of the entities that participate in conversations about science, efforts to translate altmetrics into impact indicators may produce highly misleading results. Here we present a systematic approach to identifying scientists on Twitter. (Author)

  15. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... Jobs Fellowships NEI Summer Intern Program Diversity In Vision Research & Ophthalmology (DIVRO) Student Training Programs To search for current job openings visit HHS USAJobs Home >> NEI for Kids >> Ask a Scientist Video Series Listen All About Vision About ...

  16. Engineers, scientists to benefit from CERN agreement

    CERN Multimedia

    2008-01-01

    Prime Minister Lawrence Gonzi will later this week sign a memorandum of understanding with the European Laboratory for Particle Physics in Geneva (CERN), the largest laboratory of its kind in the world, which will create new opportunities for Maltese engineers and scientists.

  17. Do Doctors differ from Medical Laboratory Scientists?

    African Journals Online (AJOL)

    Background: Doctors and laboratory scientists are at risk of infection from blood borne pathogens during routine clinical duties. After over 20 years of standard precautions, health care workers knowledge and compliance is not adequate. Aim: This study is aimed at comparing adherence and knowledge of standard ...

  18. A scientist's guide to engaging decision makers

    Science.gov (United States)

    Vano, J. A.

    2015-12-01

    Being trained as a scientist provides many valuable tools needed to address society's most pressing environmental issues. It does not, however, provide training on one of the most critical for translating science into action: the ability to engage decision makers. Engagement means different things to different people and what is appropriate for one project might not be for another. However, recent reports have emphasized that for research to be most useful to decision making, engagement should happen at the beginning and throughout the research process. There are an increasing number of boundary organizations (e.g., NOAA's Regional Integrated Sciences and Assessment program, U.S. Department of the Interior's Climate Science Centers) where engagement is encouraged and rewarded, and scientists are learning, often through trial and error, how to effectively include decision makers (a.k.a. stakeholders, practitioners, resource managers) in their research process. This presentation highlights best practices and practices to avoid when scientists engage decision makers, a list compiled through the personal experiences of both scientists and decision makers and a literature review, and how this collective knowledge could be shared, such as through a recent session and role-playing exercise given at the Northwest Climate Science Center's Climate Boot Camp. These ideas are presented in an effort to facilitate conversations about how the science community (e.g., AGU researchers) can become better prepared for effective collaborations with decision makers that will ultimately result in more actionable science.

  19. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... other programs with respect to blinding eye diseases, visual disorders, mechanisms of visual function, preservation of sight, and the special health ... Eye Ask a Scientist Video Series Glossary The Visual System Your Eyes’ Natural Defenses Eye Health and ...

  20. New Zealand scientists in firing line

    CERN Multimedia

    2003-01-01

    "Kiwi scientists have a great chance to have their work bombarded with protons and to participate in world-class particle physics research, with the signing of a Memorandum of Understanding (MoU) between CERN (the European Organisation for Nuclear Research) and New Zealand" (1/2 page)

  1. Information and Communication Network Among Natural Scientists ...

    African Journals Online (AJOL)

    This study tries to find out the extent of information and communication networks among natural scientists in Ahmadu Bello University, Zaria. Their ways of information sharing, and the extent of their participation in information networking were investigated. Using two (2) research questions, data was collected from 299 pure ...

  2. LILAVATI'S DAUGHTERS: THE WOMEN SCIENTISTS OF INDIA ...

    Indian Academy of Sciences (India)

    ranjeetha

    LILAVATI'S DAUGHTERS: THE WOMEN SCIENTISTS OF INDIA. Edited by: Rohini Godbole and Ram Ramaswamy. Published by: Indian Academy of Sciences. ISBN 978-81-8465-005-1. No. of pages: 386 (paperback). Price: Rs. 300/- US $25/- (inclusive of postage). Details for ordering and procuring the book: Address for ...

  3. Scientists' internal models of the greenhouse effect

    Science.gov (United States)

    Libarkin, J. C.; Miller, H.; Thomas, S. R.

    2013-12-01

    A prior study utilized exploratory factor analysis to identify models underlying drawings of the greenhouse effect made by entering university freshmen. This analysis identified four archetype models of the greenhouse effect that appear within the college enrolling population. The current study collected drawings made by 144 geoscientists, from undergraduate geoscience majors through professionals. These participants scored highly on a standardized assessment of climate change understanding and expressed confidence in their understanding; many also indicated that they teach climate change in their courses. Although geoscientists held slightly more sophisticated greenhouse effect models than entering freshmen, very few held complete, explanatory models. As with freshmen, many scientists (44%) depict greenhouse gases in a layer in the atmosphere; 52% of participants depicted this or another layer as a physical barrier to escaping energy. In addition, 32% of participants indicated that incoming light from the Sun remains unchanged at Earth's surface, in alignment with a common model held by students. Finally, 3-20% of scientists depicted physical greenhouses, ozone, or holes in the atmosphere, all of which correspond to non-explanatory models commonly seen within students and represented in popular literature. For many scientists, incomplete models of the greenhouse effect are clearly enough to allow for reasoning about climate change. These data suggest that: 1) better representations about interdisciplinary concepts, such as the greenhouse effect, are needed for both scientist and public understanding; and 2) the scientific community needs to carefully consider how much understanding of a model is needed before necessary reasoning can occur.

  4. Artists Create Puzzles, Scientists Solve Them.

    Science.gov (United States)

    Goldstein, Joseph L

    2017-09-21

    The Spanish artist Diego Velázquez created a puzzle-painting 360 years ago that to this day remains unsolved, but still mystifies and intrigues. Unlike artists who get their thrills by creating puzzles that stimulate the imagination, scientists get their kicks by solving puzzles that advance biomedical research. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Scientists hope collider makes a big bang

    CERN Multimedia

    Nickerson, Colin

    2007-01-01

    "In a 17-ile circular tunnel curving beneath the Swiss-French border, scientists are poised to recreate the universe's first trillionth of a second. The aim of the audacious undertaking is to solve one of the most perturbing puzzles of physics: How did matter attain mass and form the cosmos? (2 pages)

  6. Methods & Strategies: Sculpt-a-Scientist

    Science.gov (United States)

    Jackson, Julie; Rich, Ann

    2014-01-01

    Elementary science experiences help develop students' views of science and scientific interests. As a result, teachers have been charged with the task of inspiring, cultivating, recruiting, and training the scientists needed to create tomorrow's innovations and solve future problems (Business Roundtable 2005). Who will these future…

  7. Challenges before Women Scientists, Technologists & Engineers

    Indian Academy of Sciences (India)

    Sastry Indrakanti

    Science and technology has been a very important factor contributing for human welfare and development. Today India is one of the countries encouraging science and technology at the grassroots level to improve the socio-economic development and the role of women scientists and engineers are being increasingly ...

  8. Challenges before Women Scientists, Technologists & Engineers

    Indian Academy of Sciences (India)

    still below the expected level. So it is necessary to ... To provide a common platform for women scientists, engineers and technologists. • to disseminate ... and Engineering fields. To understand the critical role of women in science and technology fields. • themes. Human Resource. Development &. Management. Agricultural.

  9. University scientists test Mars probe equipment

    CERN Multimedia

    2002-01-01

    Scientists at Leicester University have spent four years researching and designing the Flight Model Position Adjustable Workbench (PAW) at the university. It will be attached to the Beagle 2 probe before being sent to the Red Planet in the spring (1/2 page).

  10. Why Frankenstein is a Stigma Among Scientists.

    Science.gov (United States)

    Nagy, Peter; Wylie, Ruth; Eschrich, Joey; Finn, Ed

    2017-06-26

    As one of the best known science narratives about the consequences of creating life, Mary Shelley's Frankenstein; or, The Modern Prometheus (1818) is an enduring tale that people know and understand with an almost instinctive familiarity. It has become a myth reflecting people's ambivalent feelings about emerging science: they are curious about science, but they are also afraid of what science can do to them. In this essay, we argue that the Frankenstein myth has evolved into a stigma attached to scientists that focalizes the public's as well as the scientific community's negative reactions towards certain sciences and scientific practices. This stigma produces ambivalent reactions towards scientific artifacts and it leads to negative connotations because it implies that some sciences are dangerous and harmful. We argue that understanding the Frankenstein stigma can empower scientists by helping them revisit their own biases as well as responding effectively to people's expectations for, and attitudes towards, scientists and scientific artifacts. Debunking the Frankenstein stigma could also allow scientists to reshape their professional identities so they can better show the public what ethical and moral values guide their research enterprises.

  11. Knowledge transfer activities of scientists in nanotechnology

    NARCIS (Netherlands)

    Zalewska-Kurek, Katarzyna; Egedova, Klaudia; Geurts, Petrus A.T.M.; Roosendaal, Hans E.

    In this paper, we present a theory of strategic positioning that explains scientists’ strategic behavior in knowledge transfer from university to industry. The theory is based on the drivers strategic interdependence and organizational autonomy and entails three modes of behavior of scientists:

  12. Galaxy Zoo: Motivations of Citizen Scientists

    Science.gov (United States)

    Raddick, M. Jordan; Bracey, Georgia; Gay, Pamela L.; Lintott, Chris J.; Cardamone, Carie; Murray, Phil; Schawinski, Kevin; Szalay, Alexander S.; Vandenberg, Jan

    2013-01-01

    Citizen science, in which volunteers work with professional scientists to conduct research, is expanding due to large online datasets. To plan projects, it is important to understand volunteers' motivations for participating. This paper analyzes results from an online survey of nearly 11000 volunteers in Galaxy Zoo, an astronomy citizen science…

  13. Towards Robot Scientists for autonomous scientific discovery.

    Science.gov (United States)

    Sparkes, Andrew; Aubrey, Wayne; Byrne, Emma; Clare, Amanda; Khan, Muhammed N; Liakata, Maria; Markham, Magdalena; Rowland, Jem; Soldatova, Larisa N; Whelan, Kenneth E; Young, Michael; King, Ross D

    2010-01-04

    We review the main components of autonomous scientific discovery, and how they lead to the concept of a Robot Scientist. This is a system which uses techniques from artificial intelligence to automate all aspects of the scientific discovery process: it generates hypotheses from a computer model of the domain, designs experiments to test these hypotheses, runs the physical experiments using robotic systems, analyses and interprets the resulting data, and repeats the cycle. We describe our two prototype Robot Scientists: Adam and Eve. Adam has recently proven the potential of such systems by identifying twelve genes responsible for catalysing specific reactions in the metabolic pathways of the yeast Saccharomyces cerevisiae. This work has been formally recorded in great detail using logic. We argue that the reporting of science needs to become fully formalised and that Robot Scientists can help achieve this. This will make scientific information more reproducible and reusable, and promote the integration of computers in scientific reasoning. We believe the greater automation of both the physical and intellectual aspects of scientific investigations to be essential to the future of science. Greater automation improves the accuracy and reliability of experiments, increases the pace of discovery and, in common with conventional laboratory automation, removes tedious and repetitive tasks from the human scientist.

  14. Massive Data Collection: Scientists' Nuggets and Basis for the Future

    Science.gov (United States)

    Kisimoto, K.

    2007-12-01

    Particularly after the advent of the multi-beam echosounders (aka, swath mapping system), accumulation of high- resolution bathymetric data invoked tremendous impact on marine sciences worldwide. In the last two decades with rapid improvements of the swath-mapping technologies, our knowledge and view of the seafloor made great advancement. Japan as a coastal state has also been conducting quite extensive and intensive "Continental Shelf Survey" for many years now and has benefited from the swath mapping technology as well. Japanese EEZ covers wide area of the northwestern Pacific and shares borders with tectonically complex and scientifically challenged neighboring regions. The "Continental Shelf Survey" of Japan is a multi-institutional effort by private, academic and governmental sectors, administered by the government. Huge amounts of marine geological, geophysical and bathymetric data are still being collected, compiled and analyzed at each sector who has its responsibility and priority, so the full access to the compiled scientific data or the disclosure of the data to science community would take some more time in future. But the parts of scientific results and data have been presented and published as they come out, at the meetings and in journals, which is also the policy of the administering government. Eyes only preview of the ongoing compiled data is not prohibited, so the international scientific cooperation discussion, for example, could be started earlier and the session like this is a best opportunity for marine scientists to be aware of what we have and what we should have for regional/global sciences to the next step, which are generally costly pursued separately. I will present and discuss on the compiled bathymetric map of the northwestern Pacific together with geophysical data or meta-data in the same region, e.g. gravity, magnetic and seismic data compiled.

  15. Scientists Involved in K-12 Education

    Science.gov (United States)

    Robigou, V.

    2004-12-01

    The publication of countless reports documenting the dismal state of science education in the 1980s, and the Third International Mathematics and Science Study (TIMMS) report (1996) called for a wider involvement of the scientific community in K-12 education and outreach. Improving science education will not happen without the collaboration of educators and scientists working in a coordinated manner and it requires a long-term, continuous effort. To contribute effectively to K-12 education all scientists should refer to the National Science Education Standards, a set of policies that guide the development of curriculum and assessment. Ocean scientists can also specifically refer to the COSEE recommendations (www.cosee.org) that led to the creation of seven regional Centers for Ocean Sciences Education Excellence. Scientists can get involved in K-12 education in a multitude of ways. They should select projects that will accommodate time away from their research and teaching obligations, their talent, and their interest but also contribute to the education reform. A few examples of effective involvement are: 1) collaborating with colleagues in a school of education that can lead to better education of all students and future teachers, 2) acting as a resource for a national program or a local science fair, 3) serving on the advisory board of a program that develops educational material, 4) speaking out at professional meetings about the value of scientists' involvement in education, 5) speaking enthusiastically about the teaching profession. Improving science education in addition to research can seem a large, overwhelming task for scientists. As a result, focusing on projects that will fit the scientist's needs as well as benefit the science reform is of prime importance. It takes an enormous amount of work and financial and personnel resources to start a new program with measurable impact on students. So, finding the right opportunity is a priority, and stepping

  16. Scientists' Perceptions of Communicating During Crises

    Science.gov (United States)

    Dohaney, J. A.; Hudson-Doyle, E.; Brogt, E.; Wilson, T. M.; Kennedy, B.

    2015-12-01

    To further our understanding of how to enhance student science and risk communication skills in natural hazards and earth science courses, we conducted a pilot study to assess the different perceptions of expert scientists and risk communication practitioners versus the perceptions of students. These differences will be used to identify expert views on best practice, and improve the teaching of communication skills at the University level. In this pilot study, a perceptions questionnaire was developed and validated. Within this, respondents (geoscientists, engineers, and emergency managers; n=44) were asked to determine their agreement with the use and effectiveness of specific communication strategies (within the first 72 hours after a devastating earthquake) when communicating to the public. In terms of strategies and information to the public, the respondents were mostly in agreement, but there were several statements which elicited large differences between expert responses: 1) the role and purpose of the scientific communication during crises (to persuade people to care, to provide advice, to empower people to take action); 2) the scientist's delivery (showing the scientists emotions and enthusiasm for scientific concepts they are discussing); and 3) the amount of data that is discussed (being comprehensive versus 'only the important' data). The most disagreed upon dimension was related to whether to disclose any political influence on the communication. Additionally, scientists identified that being an effective communicator was an important part of their job, and agreed that it is important to practice these skills. Respondents generally indicated that while scientists should be accountable for the science advice provided, they should not be held liable.

  17. Everyone Knows What a Scientist Looks Like: The Image of a Modern Scientist

    Science.gov (United States)

    Enevoldsen, A. A. G.

    2008-11-01

    Children are inspired to follow career paths when they can imagine themselves there. Seeing pictures of adult individuals who look like them working in a given career can provide this spark to children's imaginations. Most (though not all) of the current available posters of scientists are of Einstein, and Einstein-like scientists. This is not representative of the current face of science. To change this, Pacific Science Center will host a photography exhibit: photographs of real, current scientists from all races, genders, beliefs, and walks of life. Photos will be taken and short biographies written by Discovery Corps Interns (Pacific Science Center's youth development program) to increase the amount of direct contact between students and scientists, and to give the exhibit an emotional connection for local teachers and families. We plan to make the photographs from this exhibit available to teachers for use in their classrooms, in addition to being displayed at Pacific Science Center during the International Year of Astronomy. The objectives of this project are to fill a need for representative photographs of scientists in the world community and to meet two of the goals of the International Year of Astronomy: to provide a modern image of science and scientists, and to improve the gender-balanced representation of scientists at all levels and promote greater involvement by under-represented minorities in scientific and engineering careers.

  18. Nobelist TD LEE Scientist Cooperation Network and Scientist Innovation Ability Model

    Directory of Open Access Journals (Sweden)

    Jin-Qing Fang

    2013-01-01

    Full Text Available Nobelist TD Lee scientist cooperation network (TDLSCN and their innovation ability are studied. It is found that the TDLSCN not only has the common topological properties both of scale-free and small-world for a general scientist cooperation networks, but also appears the creation multiple-peak phenomenon for number of published paper with year evolution, which become Nobelist TD Lee’s significant mark distinguished from other scientists. This new phenomenon has not been revealed in the scientist cooperation networks before. To demonstrate and explain this new finding, we propose a theoretical model for a nature scientist and his/her team innovation ability. The theoretical results are consistent with the empirical studies very well. This research demonstrates that the model has a certain universality and can be extended to estimate innovation ability for any nature scientist and his/her team. It is a better method for evaluating scientist innovation ability and his/her team for the academic profession and is of application potential.

  19. Not going it alone: scientists and their work featured online at FrontierScientists

    Science.gov (United States)

    O'Connell, E. A.; Nielsen, L.

    2015-12-01

    Science outreach demystifies science, and outreach media gives scientists a voice to engage the public. Today scientists are expected to communicate effectively not only with peers but also with a braod public audience, yet training incentiives are sometimes scarce. Media creation training is even less emphasized. Editing video to modern standards takes practice; arrangling light and framing shots isn't intuitive. While great tutorials exist, learning videography, story boarding, editing and sharing techniques will always require a commitment of time and effort. Yet ideally sharing science should be low-hanging fruit. FrontierScientists, a science-sharing website funded by the NSF, seeks to let scientists display their breakthroughs and share their excitement for their work with the public by working closely yet non-exhaustively with a professional media team. A director and videographer join scientists to film first-person accounts in the field or lab. Pictures and footage with field site explanations give media creators raw material. Scientists communicate efficiently and retain editorial control over the project, but a small team of media creators craft the public aimed content. A series of engaging short videos with narrow focuses illuminate the science. Written articles support with explanations. Social media campaigns spread the word, link content, welcome comments and keep abreast of changing web requirements. All FrontierScientists featured projects are aggregated to one mobile-friendly site available online or via an App. There groupings of Arctic-focused science provide a wealth of topics and content to explore. Scientists describe why their science is important, what drew them to it, and why the average American should care. When scientists share their work it's wonderful; a team approach is a schedule-friendly way that lets them serve as science communicators without taking up a handful of extra careers.

  20. Information needs of academic medical scientists at Chulalongkorn University.

    OpenAIRE

    Premsmit, P

    1990-01-01

    The information needs of scientists in English-speaking countries have been studied and reported in the library literature. However, few studies exist on the information-seeking patterns of scientists in developing countries, and no study has examined the information needs of medical scientists in developing Asian countries. This study investigated the information needs of academic medical scientists at Chulalongkorn University in Bangkok, Thailand. The results indicate that medical scientist...

  1. Epigenome-wide association analysis revealed that SOCS3 methylation influences the effect of cumulative stress on obesity.

    Science.gov (United States)

    Xu, Ke; Zhang, Xinyu; Wang, Zuoheng; Hu, Ying; Sinha, Rajita

    2018-01-01

    Chronic stress has a significant impact on obesity. However, how stress influences obesity remains unclear. We conducted an epigenome-wide DNA methylation association analysis of obesity (N=510) and examined whether cumulative stress influenced the DNA methylation on body weight. We identified 20 CpG sites associated with body mass index at the false discovery rate qstress contributed to variations in body weight (p=0.002). Individuals with at least five major life events and lower methylation of cg1818703 showed a 1.38-fold higher risk of being obese (95%CI: 1.17-1.76). Our findings suggest that aberrant in DNA methylation is associated with body weight and that methylation of SOCS3 moderates the effect of cumulative stress on obesity. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. A simulation study on power of epigenome-wide association analysis using disease-discordant twin design

    DEFF Research Database (Denmark)

    Li, Weilong; Baumbach, Jan; Christiansen, Lene

    Background Identical twin pairs discordant for a disease have been widely used in epigenome-wide association studies (EWAS) of complex diseases because the underlying genetic background is cancelled out. Although the twin design is deemed to have enriched power as compared with ordinary case......-control design, its statistical power has not been well investigated. Methods We perform a computer simulation study on the power of the disease discordant twin design assuming that both genetic and environmental factors contribute to the liability of a disease phenotype. Power is assessed under different levels...... of genetic contribution or heritability for various effect sizes of environmental exposure that induce change in the level and variance of the normal-distributed M value of DNA methylation. Results In general, the discordant twin design outperforms ordinary case-control design especially for CpG sites...

  3. High-fat diet reprograms the epigenome of rat spermatozoa and transgenerationally affects metabolism of the offspring

    DEFF Research Database (Denmark)

    de Castro Barbosa, Thais; Ingerslev, Lars R; Alm, Petter S

    2016-01-01

    OBJECTIVES: Chronic and high consumption of fat constitutes an environmental stress that leads to metabolic diseases. We hypothesized that high-fat diet (HFD) transgenerationally remodels the epigenome of spermatozoa and metabolism of the offspring. METHODS: F0-male rats fed either HFD or chow diet...... for 12 weeks were mated with chow-fed dams to generate F1 and F2 offspring. Motile spermatozoa were isolated from F0 and F1 breeders to determine DNA methylation and small non-coding RNA (sncRNA) expression pattern by deep sequencing. RESULTS: Newborn offspring of HFD-fed fathers had reduced body weight......1 male offspring showed common DNA methylation and small non-coding RNA expression signatures. Altered expression of sperm miRNA let-7c was passed down to metabolic tissues of the offspring, inducing a transcriptomic shift of the let-7c predicted targets. CONCLUSION: Our results provide insight...

  4. Nuclear Targeting Terms for Engineers and Scientists

    Energy Technology Data Exchange (ETDEWEB)

    St Ledger, John W. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-02-01

    The Department of Defense has a methodology for targeting nuclear weapons, and a jargon that is used to communicate between the analysts, planners, aircrews, and missile crews. The typical engineer or scientist in the Department of Energy may not have been exposed to the nuclear weapons targeting terms and methods. This report provides an introduction to the terms and methodologies used for nuclear targeting. Its purpose is to prepare engineers and scientists to participate in wargames, exercises, and discussions with the Department of Defense. Terms such as Circular Error Probable, probability of hit and damage, damage expectancy, and the physical vulnerability system are discussed. Methods for compounding damage from multiple weapons applied to one target are presented.

  5. Kristian Birkeland the first space scientist

    CERN Document Server

    Egeland, Alv

    2005-01-01

    At the beginning of the 20th century Kristian Birkeland (1867-1917), a Norwegian scientist of insatiable curiosity, addressed questions that had vexed European scientists for centuries. Why do the northern lights appear overhead when the Earth’s magnetic field is disturbed? How are magnetic storms connected to disturbances on the Sun? To answer these questions Birkeland interpreted his advance laboratory simulations and daring campaigns in the Arctic wilderness in the light of Maxwell’s newly discovered laws of electricity and magnetism. Birkeland’s ideas were dismissed for decades, only to be vindicated when satellites could fly above the Earth’s atmosphere. Faced with the depleting stocks of Chilean saltpeter and the consequent prospect of mass starvation, Birkeland showed his practical side, inventing the first industrial scale method to extract nitrogen-based fertilizers from the air. Norsk Hydro, one of modern Norway’s largest industries, stands as a living tribute to his genius. Hoping to demo...

  6. Conservation beyond science: scientists as storytellers

    Directory of Open Access Journals (Sweden)

    Diogo Veríssimo

    2014-11-01

    Full Text Available As scientists we are often unprepared and unwilling to communicate our passion for what we do to those outside our professional circles. Scientific literature can also be difficult or unattractive to those without a professional interest in research. Storytelling can be a successful approach to enable readers to engage with the challenges faced by scientists. In an effort to convey to the public what it means to be a field biologist, 18 Portuguese biologists came together to write a book titled “BIOgraphies: The lives of those who study life”, in the original Portuguese “BIOgrafias: Vidas de quem estuda a vida”. This book is a collection of 35 field stories that became career landmarks for those who lived them. We discuss the obstacles and opportunities of the publishing process and reflect on the lessons learned for future outreach efforts.

  7. Early- and late-onset preeclampsia and the tissue-specific epigenome of the placenta and newborn.

    Science.gov (United States)

    Herzog, Emilie M; Eggink, Alex J; Willemsen, Sten P; Slieker, Roderick C; Wijnands, Kim P J; Felix, Janine F; Chen, Jun; Stubbs, Andrew; van der Spek, Peter J; van Meurs, Joyce B; Steegers-Theunissen, Régine P M

    2017-10-01

    Preeclampsia (PE) carries increased risks of cardiovascular- and metabolic diseases in mothers and offspring during the life course. While the severe early-onset PE (EOPE) phenotype originates from impaired placentation in early pregnancy, late-onset PE (LOPE) is in particular associated with pre-existing maternal cardiovascular- and metabolic risk factors. We hypothesize that PE is associated with altered epigenetic programming of placental and fetal tissues and that these epigenetic changes might elucidate the increased cardiovascular- and metabolic disease susceptibility in PE offspring. A nested case-control study was conducted in The Rotterdam Periconceptional Cohort comprising 13 EOPE, 16 LOPE, and three control groups of 36 uncomplicated pregnancies, 27 normotensive fetal growth restricted and 20 normotensive preterm birth (PTB) complicated pregnancies. Placental tissue, newborn umbilical cord white blood cells (UC-WBC) and umbilical vein endothelial cells were collected and DNA methylation of cytosine-guanine dinucleotides was measured by the Illumina HumanMethylation450K BeadChip. An epigenome-wide analysis was performed by using multiple linear regression models. Epigenome-wide tissue-specific analysis between EOPE and PTB controls revealed 5001 mostly hypermethylated differentially methylated positions (DMPs) in UC-WBC and 869 mostly hypomethylated DMPs in placental tissue, situated in or close to genes associated with cardiovascular-metabolic developmental pathways. This study shows differential methylation in UC-WBC and placental tissue in EOPE as compared to PTB, identifying DMPs that are associated with cardiovascular system pathways. Future studies should examine these loci and pathways in more detail to elucidate the associations between prenatal PE exposure and the cardiovascular disease risk in offspring. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  8. Modern physics for scientists and engineers

    CERN Document Server

    Morrison, John C

    2010-01-01

    Intended for a first course in modern physics, following an introductory course in physics with calculus, Modern Physics for Scientists and Engineers begins with a brief and focused account of the historical events leading to the formulation of modern quantum theory, while later chapters delve into the underlying physics. Streamlined content, chapters on semiconductors, Dirac Equation and Quantum Field Theory, and a robust pedagogy and ancillary package including an accompanying website with computer applets assists students in learning the essential material.

  9. Interactive conference of young scientists 2011. Posters

    International Nuclear Information System (INIS)

    2011-05-01

    This interactive conference of young scientists was realised on the Internet. Conference proceeded in seven sections: (1) Cellular metabolism, physiology, molecular biology and genetics; (2) Biotechnology and food technology; (3) The use of instrumental methods in the analysis of biologically important substances; (4) Organic, bio-organic and pharmaceuticals chemistry, pharmacology; (5) Ecology and environmental science; (6) Biophysics, mathematic modelling, biostatistics; (7) Open section for students. Relevant posters were included into the database INIS.

  10. Space groups for solid state scientists

    CERN Document Server

    Glazer, Michael

    2013-01-01

    This comprehensively revised - essentially rewritten - new edition of the 1990 edition (described as ""extremely useful"" by MATHEMATICAL REVIEWS and as ""understandable and comprehensive"" by Scitech) guides readers through the dense array of mathematical information in the International Tables Volume A. Thus, most scientists seeking to understand a crystal structure publication can do this from this book without necessarily having to consult the International Tables themselves. This remains the only book aimed at non-crystallographers devoted to teaching them about crystallogr

  11. Cultural isolation of third-world scientists

    International Nuclear Information System (INIS)

    Sadiq, A.

    1981-10-01

    The isolation of third world scientists from the modes of production and from the culture of their countries seems to be related to the alienation of the urban culture of these countries from their respective rural backgrounds. It is suggested that this alienation may be overcome by directly interfacing modern science and technology to the corresponding elements in their rural culture through the process of education. (author)

  12. Opinion: the basic scientist in radiology

    International Nuclear Information System (INIS)

    Holloway, A.F.; Taylor, K.W.

    1984-01-01

    Diagnostic radiology has experienced many scientific and technical advances in the past decade. New imaging methods have allowed diagnostic procedures that have in some cases produced marked advances in treatment of disease. The complexity of the science and technology requires increased knowledge of equipment and techniques on the part of users. This, together with the necessity of exploration of other new developments in science and technology, requires a closer relationship between radiologists on the one hand and basic scientists on the other. (author)

  13. What Scientists Who Study Emotion Agree About.

    Science.gov (United States)

    Ekman, Paul

    2016-01-01

    In recent years, the field of emotion has grown enormously-recently, nearly 250 scientists were identified who are studying emotion. In this article, I report a survey of the field, which revealed high agreement about the evidence regarding the nature of emotion, supporting some of both Darwin's and Wundt's 19th century proposals. Topics where disagreements remain were also exposed. © The Author(s) 2015.

  14. Reaching the Next Generation of Marine Scientists

    Science.gov (United States)

    Joyce, J.

    2009-04-01

    The next generation of marine scientists are today at primary school, secondary school or at college. To encourage them in their career, and to introduce those who are as yet undecided to the wonders of marine science, the Irish Marine Institute has devised a series of three overlapping outreach programmes to reach children at all three levels. Beginning at primary school, the "Explorers" programme offers a range of resources to teachers to enable them to teach marine-related examples as part of the science or geography modules of the SESE curriculum. These include teacher training, expert visits to schools, the installation and stocking of aquaria, field trips and downloadable lesson plans. For older pupils, the "Follow the Fleet" programme is a web-based education asset that allows users to track individual merchant ships and research vessels across the world, to interact with senior crew members of ships and to learn about their cargoes, the ports they visit and the sea conditions along the way. Finally, the "Integrated Marine Exploration Programme (IMEP)" takes secondary school pupils and university students to sea aboard the Marine Institute's research vessels to give them a taste of life as a marine scientist or to educate them in the practical day-to-day sampling and data processing tasks that make up a marine scientist's job.

  15. The scientist's role in the nuclear debate

    International Nuclear Information System (INIS)

    Blackstein, F.P.

    1981-01-01

    Until recently the public had little time for, or interest in, studying scientific developments. Details on topics such as medical research, energy developments and communications advances were left to scientific journals and specialist conferences. For the most part the public had faith in science and science was able to maintain that faith through developments which recognizably improved the lot of mankind. But faith is no longer sufficient; scientists must now interact with people if we are to fulfil our obligations in this new theatre of increased public awareness. Scientists and egineers like myself and my colleagues at Atomic Energy of Canada Ltd. are communicating with the public as one part of a broad programme of public information. This includes: operation of public information centres, visits to our laboratories, interaction with teachers, distribution of reports and hosting exhibits. Technical people have a lot to learn about communicating with the public, the media and the critics. It is an extremely difficult task, but as concerned scientists it is something we should and must do, openly and constructively

  16. Tracking Nemo: Help Scientists Understand Zebrafish Behavior.

    Science.gov (United States)

    Tolbert, Tyrone J; Nakayama, Shinnosuke; Porfiri, Maurizio

    2018-02-22

    The advent of automated tracking software has significantly reduced the time required to record movement trajectories, thereby facilitating behavioral studies of zebrafish. However, results are substantially influenced by tracking errors, such as loss and misidentification of individuals. In this study, we present the development of an online citizen science platform, Tracking Nemo, to improve data accuracy on swimming trajectories of zebrafish groups. As an online extension of software for tracking the position of zebrafish from video recordings, Tracking Nemo offers volunteers the opportunity to contribute to science by manually correcting tracked trajectory data from their personal computers. Researchers can upload their videos that require human intervention for correcting and validating the data. Citizen scientists can monitor their contributions through a leaderboard system, which is designed to strengthen participant retention and contribution by tapping into intrinsic and extrinsic motivations. Tracking Nemo is expected to help scientists improve data accuracy through the involvement of citizen scientists, who, in turn, engage in an authentic research activity and learn more about the behavior of zebrafish.

  17. Onomastic Mapping

    Directory of Open Access Journals (Sweden)

    Yuliana Yu. Gordova

    2012-12-01

    Full Text Available Mapping the onomastic material and creating linguistic atlases of each region remains a significant and urgent problem of Russian onomastics. The paper summarizes the experience of onomastic cartography, and explains the concept of onomastic map as well as linguistic and technical principles of mapping. The author considers traditional objects of mapping and main map topics and describes new opportunities which become possible due to the creation of modern means and techniques of mapping. The paper is illustrated with toponymic maps, compiled by different researchers between 1970 and 2000.

  18. Supporting Students as Scientists: One Mission's Efforts

    Science.gov (United States)

    Taylor, J.; Chambers, L. H.; Trepte, C. R.

    2012-12-01

    NASA's CALIPSO satellite mission provides an array of opportunities for teachers, students, and the general public. In developing our latest plan for education and public outreach, CALIPSO focused on efforts that would support students as scientists. CALIPSO EPO activities are aimed at inspiring young scientists through multiple avenues of potential contact, including: educator professional development, student-scientist mentoring, curriculum resource development, and public outreach through collaborative mission efforts. In this session, we will explore how these avenues complement one another and take a closer look at the development of the educator professional development activities. As part of CALIPSO's EPO efforts, we have developed the GLOBE Atmosphere Investigations Programs (AIP). The program encourages students to engage in authentic science through research on the atmosphere. The National Research Council (NRC) has emphasized the importance of teaching scientific inquiry in the National Science Education Standards (1996, 2000) and scientific practice in the recent Framework for K-12 Science Education (2011). In order to encourage student-centered science inquiry, teacher training utilizing GLOBE Atmosphere Investigations and GLOBE's Student Research Process are provided to middle and high school teachers to assist them in incorporating real scientific investigations into their classroom. Through participation in the program, teachers become a part of GLOBE (Global Learning and Observations to Benefit the Environment) - an international community of teachers, students, and scientists studying environmental science in over 24,000 schools around the world. The program uses NASA's satellites and the collection of atmosphere data by students to provide an engaging science learning experience for the students, and teachers. The GLOBE Atmosphere Investigations program offers year-long support to both teachers and students through direct involvement with NASA

  19. Scientists' Views about Attribution of Global Warming

    Science.gov (United States)

    Verheggen, Bart; Strengers, Bart; Cook, John; van Dorland, Rob; Vringer, Kees; Peters, Jeroen; Visser, Hans; Meyer, Leo

    2015-04-01

    What do scientists think? That is an important question when engaging in science communication, in which an attempt is made to communicate the scientific understanding to a lay audience. To address this question we undertook a large and detailed survey among scientists studying various aspects of climate change , dubbed "perhaps the most thorough survey of climate scientists ever" by well-known climate scientist and science communicator Gavin Schmidt. Among more than 1800 respondents we found widespread agreement that global warming is predominantly caused by human greenhouse gases. This consensus strengthens with increased expertise, as defined by the number of self-reported articles in the peer-reviewed literature. 90% of respondents with more than 10 climate-related peer-reviewed publications (about half of all respondents), agreed that anthropogenic greenhouse gases are the dominant cause of recent global warming, i.e. having contributed more than half of the observed warming. With this survey we specified what the consensus position entails with much greater specificity than previous studies. The relevance of this consensus for science communication will be discussed. Another important result from our survey is that the main attribution statement in IPCC's fourth assessment report (AR4) may lead to an underestimate of the greenhouse gas contribution to warming, because it implicitly includes the lesser known masking effect of cooling aerosols. This shows the importance of the exact wording in high-profile reports such as those from IPCC in how the statement is perceived, even by fellow scientists. The phrasing was improved in the most recent assessment report (AR5). Respondents who characterized the human influence on climate as insignificant, reported having the most frequent media coverage regarding their views on climate change. This shows that contrarian opinions are amplified in the media in relation to their prevalence in the scientific community. This

  20. Professionals and Emerging Scientists Sharing Science

    Science.gov (United States)

    Graff, P. V.; Allen, J. S.; Tobola, K.

    2010-01-01

    The Year of the Solar System (YSS) celebration begins in the fall of 2010. As YSS provides a means in which NASA can inspire members of the public about exciting missions to other worlds in our solar system, it is important to remember these missions are about the science being conducted and new discoveries being made. As part of the Year of the Solar System, Astromaterials Research and Exploration Science (ARES) Education, at the NASA Johnson Space Center, will infuse the great YSS celebration within the Expedition Earth and Beyond Program. Expedition Earth and Beyond (EEAB) is an authentic research program for students in grades 5-14 and is a component of ARES Education. Students involved in EEAB have the opportunity to conduct and share their research about Earth and/or planetary comparisons. ARES Education will help celebrate this exciting Year of the Solar System by inviting scientists to share their science. Throughout YSS, each month will highlight a topic related to exploring our solar system. Additionally, special mission events will be highlighted to increase awareness of the exciting missions and exploration milestones. To bring this excitement to classrooms across the nation, the Expedition Earth and Beyond Program and ARES Education will host classroom connection events in which scientists will have an opportunity to share discoveries being made through scientific research that relate to the YSS topic of the month. These interactive presentations will immerse students in some of the realities of exploration and potentially inspire them to conduct their own investigations. Additionally, scientists will share their own story of how they were inspired to pursue a STEM-related career that got them involved in exploration. These career highlights will allow students to understand and relate to the different avenues that scientists have taken to get where they are today. To bring the sharing of science full circle, student groups who conduct research by

  1. Scientists feature their work in Arctic-focused short videos by FrontierScientists

    Science.gov (United States)

    Nielsen, L.; O'Connell, E.

    2013-12-01

    Whether they're guiding an unmanned aerial vehicle into a volcanic plume to sample aerosols, or documenting core drilling at a frozen lake in Siberia formed 3.6 million years ago by a massive meteorite impact, Arctic scientists are using video to enhance and expand their science and science outreach. FrontierScientists (FS), a forum for showcasing scientific work, produces and promotes radically different video blogs featuring Arctic scientists. Three- to seven- minute multimedia vlogs help deconstruct researcher's efforts and disseminate stories, communicating scientific discoveries to our increasingly connected world. The videos cover a wide range of current field work being performed in the Arctic. All videos are freely available to view or download from the FrontierScientists.com website, accessible via any internet browser or via the FrontierScientists app. FS' filming process fosters a close collaboration between the scientist and the media maker. Film creation helps scientists reach out to the public, communicate the relevance of their scientific findings, and craft a discussion. Videos keep audience tuned in; combining field footage, pictures, audio, and graphics with a verbal explanation helps illustrate ideas, allowing one video to reach people with different learning strategies. The scientists' stories are highlighted through social media platforms online. Vlogs grant scientists a voice, letting them illustrate their own work while ensuring accuracy. Each scientific topic on FS has its own project page where easy-to-navigate videos are featured prominently. Video sets focus on different aspects of a researcher's work or follow one of their projects into the field. We help the scientist slip the answers to their five most-asked questions into the casual script in layman's terms in order to free the viewers' minds to focus on new concepts. Videos are accompanied by written blogs intended to systematically demystify related facts so the scientists can focus

  2. Impact of a Scientist-Teacher Collaborative Model on Students, Teachers, and Scientists

    Science.gov (United States)

    Shein, Paichi Pat; Tsai, Chun-Yen

    2015-09-01

    Collaborations between the K-12 teachers and higher education or professional scientists have become a widespread approach to science education reform. Educational funding and efforts have been invested to establish these cross-institutional collaborations in many countries. Since 2006, Taiwan initiated the High Scope Program, a high school science curriculum reform to promote scientific innovation and inquiry through an integration of advanced science and technology in high school science curricula through partnership between high school teachers and higher education scientists and science educators. This study, as part of this governmental effort, a scientist-teacher collaborative model (STCM) was constructed by 8 scientists and 4 teachers to drive an 18-week high school science curriculum reform on environmental education in a public high school. Partnerships between scientists and teachers offer opportunities to strengthen the elements of effective science teaching identified by Shulman and ultimately affect students' learning. Mixed methods research was used for this study. Qualitative methods of interviews were used to understand the impact on the teachers' and scientists' science teaching. A quasi-experimental design was used to understand the impact on students' scientific competency and scientific interest. The findings in this study suggest that the use of the STCM had a medium effect on students' scientific competency and a large effect on students' scientific individual and situational interests. In the interviews, the teachers indicated how the STCM allowed them to improve their content knowledge and pedagogical content knowledge (PCK), and the scientists indicated an increased knowledge of learners, knowledge of curriculum, and PCK.

  3. Crowdsourcing Austrian data on decomposition with the help of citizen scientists

    Science.gov (United States)

    Sandén, Taru; Berthold, Helene; Schwarz, Michael; Baumgarten, Andreas; Spiegel, Heide

    2017-04-01

    Decay of organic material, decomposition, is a critical process for life on earth. Through decomposition, food becomes available for plants and soil organisms that they use in their growth and maintenance. When plant material decomposes, it loses weight and releases the greenhouse gas carbon dioxide (CO2) into the atmosphere. Terrestrial soils contain about three times more carbon than the atmosphere and, therefore, changes in the balance of soil carbon storage and release can significantly amplify or attenuate global warming. Many factors affecting the global carbon cycle are already known and mapped; however, an index for decomposition rate is still missing, even though it is needed for climate modelling. The Tea Bag Index (TBI) measures decomposition in a standardised, achievable, climate-relevant, and time-relevant way by burying commercial nylon tea bags in soils for three months (Keuskamp et al., 2013). In the summer of 2016, TBI (expressed as decomposition rate (k) and stabilisation index (S)) was measured with the help of Austrian citizen scientists at 7-8 cm soil depth in three different land uses (maize croplands, grasslands and forests). In total ca. 2700 tea bags were sent to the citizen scientists of which ca. 50% were returned. The data generated by the citizen scientists will be incorporated into an Austrian as well as a global soil map of decomposition. This map can be used as input to improve climate modelling in the future.

  4. CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants

    DEFF Research Database (Denmark)

    Spisák, Sándor; Lawrenson, Kate; Fu, Yanfang

    2015-01-01

    The vast majority of disease-associated single-nucleotide polymorphisms (SNPs) mapped by genome-wide association studies (GWASs) are located in the non-protein-coding genome, but establishing the functional and mechanistic roles of these sequence variants has proven challenging. Here we describe ...

  5. Data sharing by scientists: Practices and perceptions

    Science.gov (United States)

    Tenopir, C.; Allard, S.; Douglass, K.; Aydinoglu, A.U.; Wu, L.; Read, E.; Manoff, M.; Frame, M.

    2011-01-01

    Background: Scientific research in the 21st century is more data intensive and collaborative than in the past. It is important to study the data practices of researchers - data accessibility, discovery, re-use, preservation and, particularly, data sharing. Data sharing is a valuable part of the scientific method allowing for verification of results and extending research from prior results. Methodology/Principal Findings: A total of 1329 scientists participated in this survey exploring current data sharing practices and perceptions of the barriers and enablers of data sharing. Scientists do not make their data electronically available to others for various reasons, including insufficient time and lack of funding. Most respondents are satisfied with their current processes for the initial and short-term parts of the data or research lifecycle (collecting their research data; searching for, describing or cataloging, analyzing, and short-term storage of their data) but are not satisfied with long-term data preservation. Many organizations do not provide support to their researchers for data management both in the short- and long-term. If certain conditions are met (such as formal citation and sharing reprints) respondents agree they are willing to share their data. There are also significant differences and approaches in data management practices based on primary funding agency, subject discipline, age, work focus, and world region. Conclusions/Significance: Barriers to effective data sharing and preservation are deeply rooted in the practices and culture of the research process as well as the researchers themselves. New mandates for data management plans from NSF and other federal agencies and world-wide attention to the need to share and preserve data could lead to changes. Large scale programs, such as the NSF-sponsored DataNET (including projects like DataONE) will both bring attention and resources to the issue and make it easier for scientists to apply sound

  6. Professional conduct of scientists during volcanic crises

    Science.gov (United States)

    IAVCEI SubcommitteeCrisis Protocols; Newhall, Chris; Aramaki, Shigeo; Barberi, Franco; Blong, Russell; Calvache, Marta; Cheminee, Jean-Louis; Punongbayan, Raymundo; Siebe, Claus; Simkin, Tom; Sparks, Stephen; Tjetjep, Barry; Newhall, Chris

    Stress during volcanic crises is high, and any friction between scientists can distract seriously from both humanitarian and scientific effort. Friction can arise, for example, if team members do not share all of their data, if differences in scientific interpretation erupt into public controversy, or if one scientist begins work on a prime research topic while a colleague with longer-standing investment is still busy with public safety work. Some problems arise within existing scientific teams; others are brought on by visiting scientists. Friction can also arise between volcanologists and public officials. Two general measures may avert or reduce friction: (a) National volcanologic surveys and other scientific groups that advise civil authorities in times of volcanic crisis should prepare, in advance of crises, a written plan that details crisis team policies, procedures, leadership and other roles of team members, and other matters pertinent to crisis conduct. A copy of this plan should be given to all current and prospective team members. (b) Each participant in a crisis team should examine his or her own actions and contribution to the crisis effort. A personal checklist is provided to aid this examination. Questions fall generally in two categories: Are my presence and actions for the public good? Are my words and actions collegial, i.e., courteous, respectful, and fair? Numerous specific solutions to common crisis problems are also offered. Among these suggestions are: (a) choose scientific team leaders primarily for their leadership skills; (b) speak publicly with a single scientific voice, especially when forecasts, warnings, or scientific disagreements are involved; (c) if you are a would-be visitor, inquire from the primary scientific team whether your help would be welcomed, and, in general, proceed only if the reply is genuinely positive; (d) in publications, personnel evaluations, and funding, reward rather than discourage teamwork. Models are

  7. How Many Women Scientists Does It Take?

    Science.gov (United States)

    Zelikova, T. J.; Ramirez, K. S.; Pendergrass, A. G.; Vijayaraghavan, R.; Weintraub, S. R.; Bohon, W.; Bartel, B. A.

    2017-12-01

    Science and activism are not mutually exclusive. In today's political and cultural landscape, scientists must become advocates. But we cannot simply support the scientific enterprise while ignoring marginalized groups in science. We must promote diversity and confront the structural inequalities and discrimination that are prevalent in science today. How do we begin to confront this challenge? 500 Women Scientists is a grassroots organization that formed in the wake of the 2016 US election. We quickly grew to more than 20,000 supporters from across the globe and moved towards a broader mission to serve society by making science open, inclusive, and accessible. Ensuring women's inclusion and an explicit consideration of diversity improves science and spurs innovation. A focus on diversity means that the best minds and talent are in the room and that we implement the most effective solutions to solve the complex global challenges we face. We accomplish our mission by bringing together communities to foster real change that comes from small groups, not large crowds. Across the world, groups of 500 Women Scientists - pods - help create deep roots through strong, personal relationships and focus on issues that resonate in their communities. Pod members meet regularly to carry out our mission through 3 types of activities: 1. Empowering women to succeed in science through mentorship, networking, and support; 2. Advocating for science through participation in marches and efforts like the "#ourEPA" and "Summer of Op-Eds" campaigns; and 3. Local outreach at schools, local community events, and more. We are building a powerful voice in conversations at the intersection of science and our most pressing issues: environmental degradation, gender politics, structural inequalities and cultural diversity. We tell our own story so that we do not remain `hidden figures,' and so that future generations can inherit and advance the knowledge that we work so hard to produce.

  8. The Impact of Scientist-Educator Collaborations: an early-career scientist's perspective

    Science.gov (United States)

    Roop, H. A.

    2017-12-01

    A decade ago, a forward-thinking faculty member exposed a group of aspiring scientists to the impacts and career benefits of working directly with K-12 students and educators. Ten years later, as one of those young scientists, it is clear that the relationships born out of this early experience can transform a researcher's impact and trajectory in science. Connections with programs like the NSF-funded PolarTREC program, the teacher-led Scientists in the Classroom effort, and through well-coordinated teacher training opportunities there are clear ways in which these partnerships can a) transform student learning; b) serve as a powerful and meaningful way to connect students to authentic research and researchers; and c) help researchers become more effective communicators by expanding their ability to connect their work to society. The distillation of science to K-12 students, with the expert eye of educators, makes scientists better at their work with tangible benefits to skills that matter in academia - securing funding, writing and communicating clearly and having high-value broader impacts. This invited abstract is submitted as part of this session's panel discussion and will explore in detail, with concrete examples, the mutual benefits of educator-scientist partnerships and how sustained engagement can transform the reach, connection and application of research science.

  9. Scientist impact factor (SIF): a new metric for improving scientists' evaluation?

    Science.gov (United States)

    Lippi, Giuseppe; Mattiuzzi, Camilla

    2017-08-01

    The publication of scientific research is the mainstay for knowledge dissemination, but is also an essential criterion of scientists' evaluation for recruiting funds and career progression. Although the most widespread approach for evaluating scientists is currently based on the H-index, the total impact factor (IF) and the overall number of citations, these metrics are plagued by some well-known drawbacks. Therefore, with the aim to improve the process of scientists' evaluation, we developed a new and potentially useful indicator of recent scientific output. The new metric scientist impact factor (SIF) was calculated as all citations of articles published in the two years following the publication year of the articles, divided by the overall number of articles published in that year. The metrics was then tested by analyzing data of the 40 top scientists of the local University. No correlation was found between SIF and H-index (r=0.15; P=0.367) or 2 years H-index (r=-0.01; P=0.933), whereas the H-index and 2 years H-index values were found to be highly correlated (r=0.57; Particles published in one year and the total number of citations to these articles in the two following years (r=0.62; Pscientists, wherein the SIF reflects the scientific output over the past two years thus increasing their chances to apply to and obtain competitive funding.

  10. Space groups for solid state scientists

    CERN Document Server

    Glazer, Michael; Glazer, Alexander N

    2014-01-01

    This Second Edition provides solid state scientists, who are not necessarily experts in crystallography, with an understandable and comprehensive guide to the new International Tables for Crystallography. The basic ideas of symmetry, lattices, point groups, and space groups are explained in a clear and detailed manner. Notation is introduced in a step-by-step way so that the reader is supplied with the tools necessary to derive and apply space group information. Of particular interest in this second edition are the discussions of space groups application to such timely topics as high-te

  11. Support for Synchrotron Access by Environmental Scientists

    International Nuclear Information System (INIS)

    Daly, Michael; Madden, Andrew; Palumbo, Anthony; Qafoku, N.

    2006-01-01

    To support ERSP-funded scientists in all aspects of synchrotron-based research at the Advanced Photon Source (APS). This support comes in one or more of the following forms: (1) writing proposals to the APS General User (GU) program, (2) providing time at MRCAT/EnviroCAT beamlines via the membership of the Molecular Environmental Science (MES) Group in MRCAT/EnviroCAT, (3) assistance in experimental design and sample preparation, (4) support at the beamline during the synchrotron experiment, (5) analysis and interpretation of the synchrotron data, and (6) integration of synchrotron experimental results into manuscripts

  12. Scientists Interacting With University Science Educators

    Science.gov (United States)

    Spector, B. S.

    2004-12-01

    Scientists with limited time to devote to educating the public about their work will get the greatest multiplier effect for their investment of time by successfully interacting with university science educators. These university professors are the smallest and least publicized group of professionals in the chain of people working to create science literate citizens. They connect to all aspects of formal and informal education, influencing everything from what and how youngsters and adults learn science to legislative rulings. They commonly teach methods of teaching science to undergraduates aspiring to teach in K-12 settings and experienced teachers. They serve as agents for change to improve science education inside schools and at the state level K-16, including what science content courses are acceptable for teacher licensure. University science educators are most often housed in a College of Education or Department of Education. Significant differences in culture exist in the world in which marine scientists function and that in which university science educators function, even when they are in the same university. Subsequently, communication and building relationships between the groups is often difficult. Barriers stem from not understanding each other's roles and responsibilities; and different reward systems, assumptions about teaching and learning, use of language, approaches to research, etc. This presentation will provide suggestions to mitigate the barriers and enable scientists to leverage the multiplier effect saving much time and energy while ensuring the authenticity of their message is maintained. Likelihood that a scientist's message will retain its authenticity stems from criteria for a university science education position. These professors have undergraduate degrees in a natural science (e.g., biology, chemistry, physics, geology), and usually a master's degree in one of the sciences, a combination of natural sciences, or a master's including

  13. Mathematics for natural scientists II advanced methods

    CERN Document Server

    Kantorovich, Lev

    2016-01-01

    This book covers the advanced mathematical techniques useful for physics and engineering students, presented in a form accessible to physics students, avoiding precise mathematical jargon and laborious proofs. Instead, all proofs are given in a simplified form that is clear and convincing for a physicist. Examples, where appropriate, are given from physics contexts. Both solved and unsolved problems are provided in each chapter. Mathematics for Natural Scientists II: Advanced Methods is the second of two volumes. It follows the first volume on Fundamentals and Basics.

  14. Social origins of american scientists and scholars.

    Science.gov (United States)

    Hardy, K R

    1974-08-09

    Data from a wide variety of sources reflect geographical, baccalaureate, and social class variations in the production of scientific and scholarly doctorates in the United States. To a significant extent, these variations are associated with the kind of religiousethnic group from which such persons come. Roman Catholics are extremely low producers of scientists and scholars, but fundamentalistic and traditional Protestant faiths (southern white Protestants, Lutherans) are also low producers. Liberal Protestant sects, such as Unitarians and Quakers, and secularized Jewish groups are highly productive, and less liberal faiths are moderately productive. Variations in productivity are reflective of differences in beliefs and values. Highly productive groups share a certain set of values, unproductive groups hold the antithesis of these, and those groups intermediate in productivity possess a mixed blend. Tentatively, the common beliefs and value systems of high producers seem to include naturalism; intrinsic valuation of learning and the individual quest for truth; emphasis on human dignity, goodness, and competence; a life pathway of serious dedication, of service to humanity, of continual striving; humanistic equalitarianism; a pragmatic search for better ways of doing things unfettered by traditional restraints; and a focus on the relatively immediate, foreseeable future which can be affected by personal effort. Historically, the scientists (or their immediate ancestors) have broken away from the traditional orthodoxy, broadened certain values, and retained others. For example, the children of Jewish immigrants to the United States departed from the traditional ritualism of the eastern European Jewish community, broadened the old value of scriptural erudition to include secular learning of all kinds, but maintained emphasis upon personal striving and social responsibility. Also, it appears that eminent scientists often emerge from devout Protestant homes emphasizing

  15. Practical Statistics for Environmental and Biological Scientists

    CERN Document Server

    Townend, John

    2012-01-01

    All students and researchers in environmental and biological sciences require statistical methods at some stage of their work. Many have a preconception that statistics are difficult and unpleasant and find that the textbooks available are difficult to understand. Practical Statistics for Environmental and Biological Scientists provides a concise, user-friendly, non-technical introduction to statistics. The book covers planning and designing an experiment, how to analyse and present data, and the limitations and assumptions of each statistical method. The text does not refer to a specific comp

  16. SCIENCE, SCIENTISTS, AND POLICY ADVOCACY - MAY 16, 2007

    Science.gov (United States)

    Effectively resolving many current ecological policy issues requires an array of scientific information. Sometimes scientific information is summarized for decision-makers by policy analysts or others, but often it comes directly from scientists. The ability of scientists (and sc...

  17. Scientists adopt new strategy to find Huntington's disease therapies

    Science.gov (United States)

    ... News Releases News Release Friday, August 7, 2015 Scientists adopt new strategy to find Huntington’s disease therapies A skyline view of Huntington’s disease. Scientists searched the chromosomes of Huntington’s disease patients to ...

  18. Attitudes and norms affecting scientists' data reuse.

    Science.gov (United States)

    Curty, Renata Gonçalves; Crowston, Kevin; Specht, Alison; Grant, Bruce W; Dalton, Elizabeth D

    2017-01-01

    The value of sharing scientific research data is widely appreciated, but factors that hinder or prompt the reuse of data remain poorly understood. Using the Theory of Reasoned Action, we test the relationship between the beliefs and attitudes of scientists towards data reuse, and their self-reported data reuse behaviour. To do so, we used existing responses to selected questions from a worldwide survey of scientists developed and administered by the DataONE Usability and Assessment Working Group (thus practicing data reuse ourselves). Results show that the perceived efficacy and efficiency of data reuse are strong predictors of reuse behaviour, and that the perceived importance of data reuse corresponds to greater reuse. Expressed lack of trust in existing data and perceived norms against data reuse were not found to be major impediments for reuse contrary to our expectations. We found that reported use of models and remotely-sensed data was associated with greater reuse. The results suggest that data reuse would be encouraged and normalized by demonstration of its value. We offer some theoretical and practical suggestions that could help to legitimize investment and policies in favor of data sharing.

  19. Math for scientists refreshing the essentials

    CERN Document Server

    Maurits, Natasha

    2017-01-01

    Accessible and comprehensive, this guide is an indispensable tool for anyone in the sciences – new and established researchers, students and scientists – looking either to refresh their math skills or to prepare for the broad range of math, statistical and data-related challenges they are likely to encounter in their work or studies. In addition to helping scientists improve their knowledge of key mathematical concepts, this unique book will help readers: ·                     Read mathematical symbols ·                     Understand formulas, data or statistical information ·                     Determine medication equivalents ·                     Analyze neuroimaging  Mathematical concepts are presented alongside illustrative and useful real-world scien­tific examples and are further clarified through practical pen-and-paper exercises. Whether you are a student encountering high-level mathematics in your research or...

  20. Attitudes and norms affecting scientists' data reuse.

    Directory of Open Access Journals (Sweden)

    Renata Gonçalves Curty

    Full Text Available The value of sharing scientific research data is widely appreciated, but factors that hinder or prompt the reuse of data remain poorly understood. Using the Theory of Reasoned Action, we test the relationship between the beliefs and attitudes of scientists towards data reuse, and their self-reported data reuse behaviour. To do so, we used existing responses to selected questions from a worldwide survey of scientists developed and administered by the DataONE Usability and Assessment Working Group (thus practicing data reuse ourselves. Results show that the perceived efficacy and efficiency of data reuse are strong predictors of reuse behaviour, and that the perceived importance of data reuse corresponds to greater reuse. Expressed lack of trust in existing data and perceived norms against data reuse were not found to be major impediments for reuse contrary to our expectations. We found that reported use of models and remotely-sensed data was associated with greater reuse. The results suggest that data reuse would be encouraged and normalized by demonstration of its value. We offer some theoretical and practical suggestions that could help to legitimize investment and policies in favor of data sharing.

  1. Anaxagoras and the Scientist/Laity Interaction

    Science.gov (United States)

    Woolf, N. J.

    The phenomenon that caused Anaxagoras to develop his model that explained the phases and eclipses of the Moon was a meteorite fall. The model was a turning point for science in explaining more than one phenomenon with a single model. It precipitated the growth of Greek astronomy and the first heliocentric theory. Anaxagoras was also the first scientist to get into trouble for a conflict between science and religion. Contrary to an impression from the title of this conference, scientific literature paid little attention to the meteorite fall phenomenon. Both scientists and the public mainly pay attention to models, and often to the extraneous irrelevant attachments of models, those by which it is placed in memory. Models are artistic creations that are culture dependent. Phenomena are our only solid link to the world of reality. The main issue of this paper is the problems that the individual has with models. The paper discusses the effect of Anaxagoras on scientific thought. It concludes by exploring three areas where relationship of science to society as Anaxagoras set it up, has left unresolved problems.

  2. Impact of Maternal Diet on the Epigenome during In Utero Life and the Developmental Programming of Diseases in Childhood and Adulthood

    Directory of Open Access Journals (Sweden)

    Ho-Sun Lee

    2015-11-01

    Full Text Available Exposure to environmental factors in early life can influence developmental processes and long-term health in humans. Early life nutrition and maternal diet are well-known examples of conditions shown to influence the risk of developing metabolic diseases, including type 2 diabetes mellitus and cardiovascular diseases, in adulthood. It is increasingly accepted that environmental compounds, including nutrients, can produce changes in the genome activity that, in spite of not altering the DNA sequence, can produce important, stable and, in some instances, transgenerational alterations in the phenotype. Epigenetics refers to changes in gene function that cannot be explained by changes in the DNA sequence, with DNA methylation patterns/histone modifications that can make important contributions to epigenetic memory. The epigenome can be considered as an interface between the genome and the environment that is central to the generation of phenotypes and their stability throughout the life course. To better understand the role of maternal health and nutrition in the initiation and progression of diseases in childhood and adulthood, it is necessary to identify the physiological and/or pathological roles of specific nutrients on the epigenome and how dietary interventions in utero and early life could modulate disease risk through epigenomic alteration.

  3. Impact of Maternal Diet on the Epigenome during In Utero Life and the Developmental Programming of Diseases in Childhood and Adulthood

    Science.gov (United States)

    Lee, Ho-Sun

    2015-01-01

    Exposure to environmental factors in early life can influence developmental processes and long-term health in humans. Early life nutrition and maternal diet are well-known examples of conditions shown to influence the risk of developing metabolic diseases, including type 2 diabetes mellitus and cardiovascular diseases, in adulthood. It is increasingly accepted that environmental compounds, including nutrients, can produce changes in the genome activity that, in spite of not altering the DNA sequence, can produce important, stable and, in some instances, transgenerational alterations in the phenotype. Epigenetics refers to changes in gene function that cannot be explained by changes in the DNA sequence, with DNA methylation patterns/histone modifications that can make important contributions to epigenetic memory. The epigenome can be considered as an interface between the genome and the environment that is central to the generation of phenotypes and their stability throughout the life course. To better understand the role of maternal health and nutrition in the initiation and progression of diseases in childhood and adulthood, it is necessary to identify the physiological and/or pathological roles of specific nutrients on the epigenome and how dietary interventions in utero and early life could modulate disease risk through epigenomic alteration. PMID:26593940

  4. Educating the Next Generation of Lunar Scientists

    Science.gov (United States)

    Shaner, A. J.; Shipp, S. S.; Allen, J. S.; Kring, D. A.

    2010-12-01

    The Center for Lunar Science and Exploration (CLSE), a collaboration between the Lunar and Planetary Institute (LPI) and NASA’s Johnson Space Center (JSC), is one of seven member teams of the NASA Lunar Science Institute (NLSI). In addition to research and exploration activities, the CLSE team is deeply invested in education and outreach. In support of NASA’s and NLSI’s objective to train the next generation of scientists, CLSE’s High School Lunar Research Project is a conduit through which high school students can actively participate in lunar science and learn about pathways into scientific careers. The High School Lunar Research Project engages teams of high school students in authentic lunar research that envelopes them in the process of science and supports the science goals of the CLSE. Most high school students’ lack of scientific research experience leaves them without an understanding of science as a process. Because of this, each team is paired with a lunar scientist mentor responsible for guiding students through the process of conducting a scientific investigation. Before beginning their research, students undertake “Moon 101,” designed to familiarize them with lunar geology and exploration. Students read articles covering various lunar geology topics and analyze images from past and current lunar missions to become familiar with available lunar data sets. At the end of “Moon 101”, students present a characterization of the geology and chronology of features surrounding the Apollo 11 landing site. To begin their research, teams choose a research subject from a pool of topics compiled by the CLSE staff. After choosing a topic, student teams ask their own research questions, within the context of the larger question, and design their own research approach to direct their investigation. At the conclusion of their research, teams present their results and, after receiving feedback, create and present a conference style poster to a panel of

  5. 1HE SCIENTISTS WILL SAVE 1HE WORLD: Environment Education ...

    African Journals Online (AJOL)

    sentiment that scientists simply provide desirable progress. A scientist's role now appears to have changed from provider of progress to that of moralist: eg. to give ... positivistic sentiment: if scientists get their act together ...... However, the literature list at the end gives information for further reading and sources of information.

  6. Pathways for impact: scientists' different perspectives on agricultural innovation

    NARCIS (Netherlands)

    Röling, N.G.

    2009-01-01

    This paper takes the viewpoint of a social scientist and looks at agricultural scientists' pathways for science impact. Awareness of these pathways is increasingly becoming part and parcel of the professionalism of the agricultural scientist, now that the pressure is on to mobilize smallholders and

  7. Investigation of the Secondary School Students' Images of Scientists

    Science.gov (United States)

    Akgün, Abuzer

    2016-01-01

    The overall purpose of this study is to explore secondary school students' images of scientists. In addition to this comprehensive purpose, it is also investigated that if these students' current images of scientists and those in which they see themselves as a scientist in the near future are consistent or not. The study was designed in line with…

  8. Identity Matching to Scientists: Differences That Make a Difference?

    Science.gov (United States)

    Andersen, Hanne Moeller; Krogh, Lars Brian; Lykkegaard, Eva

    2014-01-01

    Students' images of science and scientists are generally assumed to influence their related subject choices and aspirations for tertiary education within science and technology. Several research studies have shown that many young people hold rather stereotypical images of scientists, making it hard for them to see themselves as future scientists.…

  9. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... with respect to blinding eye diseases, visual disorders, mechanisms of visual function, preservation of sight, and the ... Contact Us A-Z Site Map NEI on Social Media Information in Spanish (Información en español) Website, ...

  10. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... Search Search the NEI Website search NEI on Social Media | Search A-Z | en español | Text size S ... Contact Us A-Z Site Map NEI on Social Media Information in Spanish (Información en español) Website, ...

  11. Scientists develop the Universe's baby pictures

    CERN Multimedia

    Overbye, D

    2002-01-01

    Using a radio telescope high in the Andes, astronomers have mapped minute variations in the brightness of radio waves thought to be left over from the Big Bang. They reveal the universe when it was only some 300,000 years old and about as hot as a cool star (2 pages).

  12. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... Search Search the NEI Website search NEI on Social Media | Search A-Z | en español | Text size S M ... Contact Us A-Z Site Map NEI on Social Media Information in Spanish (Información en español) Website, Social ...

  13. Ask a Scientist: What is Color Blindness?

    Medline Plus

    Full Text Available ... questions Clinical Studies Publications Catalog Photos and Images Spanish Language Information Grants and Funding Extramural Research Division ... Site Map NEI on Social Media Information in Spanish (Información en español) Website, Social Media Policies and ...

  14. Preparing Scientists to be Community Partners

    Science.gov (United States)

    Pandya, R. E.

    2012-12-01

    Many students, especially students from historically under-represented communities, leave science majors or avoid choosing them because scientific careers do not offer enough opportunity to contribute to their communities. Citizen science, or public participation in scientific research, may address these challenges. At its most collaborative, it means inviting communities to partner in every step of the scientific process from defining the research question to applying the results to community priorities. In addition to attracting and retaining students, this level of community engagement will help diversify science, ensure the use and usability of our science, help buttress public support of science, and encourage the application of scientific results to policy. It also offers opportunities to tackle scientific questions that can't be accomplished in other way and it is demonstrably effective at helping people learn scientific concepts and methods. In order to learn how to prepare scientists for this kind of intensive community collaboration, we examined several case studies, including a project on disease and public health in Africa and the professionally evaluated experience of two summer interns in Southern Louisiana. In these and other cases, we learned that scientific expertise in a discipline has to be accompanied by a reservoir of humility and respect for other ways of knowing, the ability to work collaboratively with a broad range of disciplines and people, patience and enough career stability to allow that patience, and a willingness to adapt research to a broader set of scientific and non-scientific priorities. To help students achieve this, we found that direct instruction in participatory methods, mentoring by community members and scientists with participatory experience, in-depth training on scientific ethics and communication, explicit articulation of the goal of working with communities, and ample opportunity for personal reflection were essential

  15. The History of Winter: teachers as scientists

    Science.gov (United States)

    Koenig, L.; Courville, Z.; Wasilewski, P. J.; Gow, T.; Bender, K. J.

    2013-12-01

    The History of Winter (HOW) is a NASA Goddard Space Flight Center-funded teacher enrichment program that was started by Dr. Peter Wasilewski (NASA), Dr. Robert Gabrys (NASA) and Dr. Tony Gow (Cold Regions Research and Engineering Laboratory, or CRREL) in 2001 and continues with support and involvement of scientists from both the NASA Cryospheric Sciences Laboratory and CREEL. The program brings educators mostly from middle and high schools but also from state parks, community colleges and other institutions from across the US to the Northwood School (a small, private boarding school) in Lake Placid, NY for one week to learn about several facets of winter, polar, and snow research, including the science and history of polar ice core research, lake ice formation and structure, snow pack science, winter ecology, and remote sensing including current and future NASA cryospheric missions. The program receives support from the Northwood School staff to facilitate the program. The goal of the program is to create 'teachers as scientists' which is achieved through several hands-on field experiences in which the teachers have the opportunity to work with polar researchers from NASA, CRREL and partner Universities to dig and sample snow pits, make ice thin sections from lake ice, make snow shelters, and observe under-ice lake ecology. The hands-on work allows the teachers to use the same tools and techniques used in polar research while simultaneously introducing science concepts and activities to support their classroom work. The ultimate goal of the program is to provide the classroom teachers with the opportunity to learn about current and timely cryospheric research as well as to engage in real fieldwork experiences. The enthusiasm generated during the week-long program is translated into classroom activities with guidance from scientists, teachers and educational professionals. The opportunity to engage with polar researchers, both young investigators and renowned

  16. Somatosensory maps.

    Science.gov (United States)

    Harding-Forrester, Samuel; Feldman, Daniel E

    2018-01-01

    Somatosensory areas containing topographic maps of the body surface are a major feature of parietal cortex. In primates, parietal cortex contains four somatosensory areas, each with its own map, with the primary cutaneous map in area 3b. Rodents have at least three parietal somatosensory areas. Maps are not isomorphic to the body surface, but magnify behaviorally important skin regions, which include the hands and face in primates, and the whiskers in rodents. Within each map, intracortical circuits process tactile information, mediate spatial integration, and support active sensation. Maps may also contain fine-scale representations of touch submodalities, or direction of tactile motion. Functional representations are more overlapping than suggested by textbook depictions of map topography. The whisker map in rodent somatosensory cortex is a canonic system for studying cortical microcircuits, sensory coding, and map plasticity. Somatosensory maps are plastic throughout life in response to altered use or injury. This chapter reviews basic principles and recent findings in primate, human, and rodent somatosensory maps. Copyright © 2018 Elsevier B.V. All rights reserved.

  17. Topographic mapping

    Science.gov (United States)

    ,

    2008-01-01

    The U.S. Geological Survey (USGS) produced its first topographic map in 1879, the same year it was established. Today, more than 100 years and millions of map copies later, topographic mapping is still a central activity for the USGS. The topographic map remains an indispensable tool for government, science, industry, and leisure. Much has changed since early topographers traveled the unsettled West and carefully plotted the first USGS maps by hand. Advances in survey techniques, instrumentation, and design and printing technologies, as well as the use of aerial photography and satellite data, have dramatically improved mapping coverage, accuracy, and efficiency. Yet cartography, the art and science of mapping, may never before have undergone change more profound than today.

  18. Impact of a Scientist-Teacher Collaborative Model on Students, Teachers, and Scientists

    Science.gov (United States)

    Shein, Paichi Pat; Tsai, Chun-Yen

    2015-01-01

    Collaborations between the K-12 teachers and higher education or professional scientists have become a widespread approach to science education reform. Educational funding and efforts have been invested to establish these cross-institutional collaborations in many countries. Since 2006, Taiwan initiated the High Scope Program, a high school…

  19. Quark Matter 2017: Young Scientist Support

    Energy Technology Data Exchange (ETDEWEB)

    Evdokimov, Olga [University of Illinois at Chicago

    2017-07-31

    Quark Matter conference series are amongst the major scientific events for the Relativistic Heavy Ion community. With over 30 year long history, the meetings are held about every 1½ years to showcase the progress made in theoretical and experimental studies of nuclear matter under extreme conditions. The 26th International Conference on Ultra-relativistic Nucleus-Nucleus Collisions (Quark Matter 2017) was held at the Hyatt Regency Hotel in downtown Chicago from Sunday, February 5th through Saturday, February 11th, 2017. The conference featured about 180 plenary and parallel presentations of the most significant recent results in the field, a poster session for additional presentations, and an evening public lecture. Following the tradition of previous Quark Matter meetings, the first day of the conference was dedicated entirely to a special program for young scientists (graduate students and postdoctoral researchers). This grant will provided financial support for 235 young physicists facilitating their attendance of the conference.

  20. Nicholson Medal Lecture: Scientists and Totalitarian Societies

    Science.gov (United States)

    Fang, Li-Zhi

    1997-04-01

    In order to call for support for his policy in China from the scientific community outside of China, Li Peng, China's premier today and at the time of Tiananmen massacre in 1989, published an editorial of ``Science" magazine (July 5, 1996) titled ``Why China needs science ... and partners." This editorial brought a serious problem, which is originally faced by scientists in a totalitarian society, upon the scientific community in free societies outside. It is well known that the current attitude of the Chinese government toward science is what it was during the years of Mao and the Soviet Union: science is limited to provide instruments useful to the rulers, but any degree of freedom, such as to challenge ideas, required by science to change the totalitarian regime itself, is suppressed. Thus, the problem facing us is: how to help your colleagues and promote science in a totalitarian society, without becoming a partner of the injustices of that regime.

  1. Microgravity sciences application visiting scientist program

    Science.gov (United States)

    Glicksman, Martin; Vanalstine, James

    1995-01-01

    Marshall Space Flight Center pursues scientific research in the area of low-gravity effects on materials and processes. To facilitate these Government performed research responsibilities, a number of supplementary research tasks were accomplished by a group of specialized visiting scientists. They participated in work on contemporary research problems with specific objectives related to current or future space flight experiments and defined and established independent programs of research which were based on scientific peer review and the relevance of the defined research to NASA microgravity for implementing a portion of the national program. The programs included research in the following areas: protein crystal growth, X-ray crystallography and computer analysis of protein crystal structure, optimization and analysis of protein crystal growth techniques, and design and testing of flight hardware.

  2. The Maturation of a Scientist: An Autobiography.

    Science.gov (United States)

    Roizman, Bernard

    2015-11-01

    I was shaped by World War II, years of near starvation as a war refugee, postwar chaos, life in several countries, and relative affluence in later life. The truth is that as I was growing up I wanted to be a writer. My aspirations came to an end when, in order to speed up my graduation from college, I took courses in microbiology. It was my second love at first sight-that of my wife preceded it. I view science as an opportunity to discover the designs in the mosaics of life. What initiates my search of discovery is an observation that makes no sense unless there exists a novel design. Once the design is revealed there is little interest in filling all the gaps. I was fortunate to understand that what lasts are not the scientific reports but rather the generations of scientists whose education I may have influenced.

  3. LAB building a home for scientists

    CERN Document Server

    Fishman, Mark C

    2017-01-01

    Laboratories are both monasteries and space stations, redolent of the great ideas of generations past and of technologies to propel the future. Yet standard lab design has changed only little over recent years. Here Mark Fishman describes how to build labs as homes for scientists, to accommodate not just their fancy tools, but also their personalities. This richly illustrated book explores the roles of labs through history, from the alchemists of the Middle Ages to the chemists of the 19th and 20th centuries, and to the geneticists and structural biologists of today, and then turns to the special features of the laboratories Fishman helped to design in Cambridge, Shanghai, and Basel. Anyone who works in, or plans to build a lab, will enjoy this book, which will encourage them to think about how this special environment drives or impedes their important work.

  4. Strategic career planning for physician-scientists.

    Science.gov (United States)

    Shimaoka, Motomu

    2015-05-01

    Building a successful professional career in the physician-scientist realm is rewarding but challenging, especially in the dynamic and competitive environment of today's modern society. This educational review aims to provide readers with five important career development lessons drawn from the business and social science literatures. Lessons 1-3 describe career strategy, with a focus on promoting one's strengths while minimizing fixing one's weaknesses (Lesson 1); effective time management in the pursuit of long-term goals (Lesson 2); and the intellectual flexibility to abandon/modify previously made decisions while embracing emerging opportunities (Lesson 3). Lesson 4 explains how to maximize the alternative benefits of English-language fluency (i.e., functions such as signaling and cognition-enhancing capabilities). Finally, Lesson 5 discusses how to enjoy happiness and stay motivated in a harsh, zero-sum game society.

  5. Climate Change: On Scientists and Advocacy

    Science.gov (United States)

    Schmidt, Gavin A.

    2014-01-01

    Last year, I asked a crowd of a few hundred geoscientists from around the world what positions related to climate science and policy they would be comfortable publicly advocating. I presented a list of recommendations that included increased research funding, greater resources for education, and specific emission reduction technologies. In almost every case, a majority of the audience felt comfortable arguing for them. The only clear exceptions were related to geo-engineering research and nuclear power. I had queried the researchers because the relationship between science and advocacy is marked by many assumptions and little clarity. This despite the fact that the basic question of how scientists can be responsible advocates on issues related to their expertise has been discussed for decades most notably in the case of climate change by the late Stephen Schneider.

  6. Business planning for scientists and engineers

    Energy Technology Data Exchange (ETDEWEB)

    Servo, J.C.; Hauler, P.D.

    1992-03-01

    Business Planning for Scientists and Engineers is a combination text/workbook intended for use by individuals and firms having received Phase II SBIR funding (Small Business Innovation Research). It is used to best advantage in combination with other aspects of the Commercialization Assistance Project developed by Dawnbreaker for the US Department of Energy. Although there are many books on the market which indicate the desired contents of a business plan, there are none which clearly indicate how to find the needed information. This book focuses on the how of business planning: how to find the needed information; how to keep yourself honest about the market potential; how to develop the plan; how to sell and use the plan.

  7. Ivan Yakovych Gorbachevsky – Scientist, Patriot, Citizen

    Directory of Open Access Journals (Sweden)

    V. M. Danilova

    2014-10-01

    Full Text Available The article presents the facts about life and research activity of Ivan Ya. Gorbachevsky (1854-1942, the prominent scientist, Ukrainian by origin, doctor of medical sciences, professor, dean of the medical faculty and the rector of Charles University in Prague, member of the health board of the Czech Kingdom, a member of the Supreme Council of Health of Austria-Hungary in Vienna, a lifelong member of the House of Lords of the Austrian Parliament, first health minister of Austria-Hungary, rector of the Ukrainian Free University in Prague, professor of chemistry at the Padebradsk Economic Academy and the Ukrainian Pedagogical Dragomanov University, AUAS member in 1925, member of the Shevchenko Scientific Society. His research works were devoted to digestion of proteins, public and food hygiene. He was the first who synthesized uric acid (1882 and discovered xanthine oxidase (1889.

  8. Modern physics for scientists and engineers

    CERN Document Server

    Morrison, John C

    2015-01-01

    The second edition of Modern Physics for Scientists and Engineers is intended for a first course in modern physics. Beginning with a brief and focused account of the historical events leading to the formulation of modern quantum theory, later chapters delve into the underlying physics. Streamlined content, chapters on semiconductors, Dirac equation and quantum field theory, as well as a robust pedagogy and ancillary package, including an accompanying website with computer applets, assist students in learning the essential material. The applets provide a realistic description of the energy levels and wave functions of electrons in atoms and crystals. The Hartree-Fock and ABINIT applets are valuable tools for studying the properties of atoms and semiconductors.

  9. Linear functional analysis for scientists and engineers

    CERN Document Server

    Limaye, Balmohan V

    2016-01-01

    This book provides a concise and meticulous introduction to functional analysis. Since the topic draws heavily on the interplay between the algebraic structure of a linear space and the distance structure of a metric space, functional analysis is increasingly gaining the attention of not only mathematicians but also scientists and engineers. The purpose of the text is to present the basic aspects of functional analysis to this varied audience, keeping in mind the considerations of applicability. A novelty of this book is the inclusion of a result by Zabreiko, which states that every countably subadditive seminorm on a Banach space is continuous. Several major theorems in functional analysis are easy consequences of this result. The entire book can be used as a textbook for an introductory course in functional analysis without having to make any specific selection from the topics presented here. Basic notions in the setting of a metric space are defined in terms of sequences. These include total boundedness, c...

  10. Ozone Gardens for the Citizen Scientist

    Science.gov (United States)

    Pippin, Margaret; Reilly, Gay; Rodjom, Abbey; Malick, Emily

    2016-01-01

    NASA Langley partnered with the Virginia Living Museum and two schools to create ozone bio-indicator gardens for citizen scientists of all ages. The garden at the Marshall Learning Center is part of a community vegetable garden designed to teach young children where food comes from and pollution in their area, since most of the children have asthma. The Mt. Carmel garden is located at a K-8 school. Different ozone sensitive and ozone tolerant species are growing and being monitored for leaf injury. In addition, CairClip ozone monitors were placed in the gardens and data are compared to ozone levels at the NASA Langley Chemistry and Physics Atmospheric Boundary Layer Experiment (CAPABLE) site in Hampton, VA. Leaf observations and plant measurements are made two to three times a week throughout the growing season.

  11. Promoting Collaborations Between Radiologists and Scientists.

    Science.gov (United States)

    Yu, John-Paul J; Spieler, Bradley M; Chan, Tiffany L; Johnson, Elizabeth M; Gulani, Vikas; Sandler, Kim L; Narayana, Ponnada A; Mar, Winnie A; Brian, James M; Ng, Chin K; Hardy, Peter A

    2018-01-01

    Radiology as a discipline thrives on the dynamic interplay between technological and clinical advances. Progress in almost all facets of the imaging sciences is highly dependent on complex tools sourced from physics, engineering, biology, and the clinical sciences to obtain, process, and view imaging studies. The application of these tools, however, requires broad and deep medical knowledge about disease pathophysiology and its relationship with medical imaging. This relationship between clinical medicine and imaging technology, nurtured and fostered over the past 75 years, has cultivated extraordinarily rich collaborative opportunities between basic scientists, engineers, and physicians. In this review, we attempt to provide a framework to identify both currently successful collaborative ventures and future opportunities for scientific partnership. This invited review is a product of a special working group within the Association of University Radiologists-Radiology Research Alliance. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

  12. Cell scientist to watch - Dana Branzei.

    Science.gov (United States)

    2017-10-01

    Originally from Iaşi, Romania, Dana received her bachelor's degree in pharmaceutical sciences and a master's degree in molecular and cellular biology from Tohoku University in Sendai, Japan. For her PhD, she joined the lab of Takemi Enomoto to work on DNA replication and recombination in yeast. After a short postdoc with Kunihiro Ohta at the RIKEN laboratory in Wako, Dana took a position as a staff scientist with Marco Foiani at the Institute of Molecular Oncology Foundation (IFOM) in Milan, Italy. There, she became a junior group leader in 2008 and tenured principal investigator in 2013. Dana was elected a member of EMBO in 2016 and has been the recipient of both a European Research Council (ERC) starting grant and an ERC consolidator grant. Her lab is interested in the mechanistic interplay of DNA damage response and regulatory pathways of chromosome structure during replication. © 2017. Published by The Company of Biologists Ltd.

  13. Mathematics for natural scientists fundamentals and basics

    CERN Document Server

    Kantorovich, Lev

    2016-01-01

    This book, the first in a two part series, covers a course of mathematics tailored specifically for physics, engineering and chemistry students at the undergraduate level. It is unique in that it begins with logical concepts of mathematics first encountered at A-level and covers them in thorough detail, filling in the gaps in students' knowledge and reasoning. Then the book aids the leap between A-level and university-level mathematics, with complete proofs provided throughout and all complex mathematical concepts and techniques presented in a clear and transparent manner. Numerous examples and problems (with answers) are given for each section and, where appropriate, mathematical concepts are illustrated in a physics context. This text gives an invaluable foundation to students and a comprehensive aid to lecturers. Mathematics for Natural Scientists: Fundamentals and Basics is the first of two volumes. Advanced topics and their applications in physics are covered in the second volume.

  14. Quantum Genetic Algorithms for Computer Scientists

    Directory of Open Access Journals (Sweden)

    Rafael Lahoz-Beltra

    2016-10-01

    Full Text Available Genetic algorithms (GAs are a class of evolutionary algorithms inspired by Darwinian natural selection. They are popular heuristic optimisation methods based on simulated genetic mechanisms, i.e., mutation, crossover, etc. and population dynamical processes such as reproduction, selection, etc. Over the last decade, the possibility to emulate a quantum computer (a computer using quantum-mechanical phenomena to perform operations on data has led to a new class of GAs known as “Quantum Genetic Algorithms” (QGAs. In this review, we present a discussion, future potential, pros and cons of this new class of GAs. The review will be oriented towards computer scientists interested in QGAs “avoiding” the possible difficulties of quantum-mechanical phenomena.

  15. The challenges for scientists in avoiding plagiarism.

    Science.gov (United States)

    Fisher, E R; Partin, K M

    2014-01-01

    Although it might seem to be a simple task for scientists to avoid plagiarism and thereby an allegation of research misconduct, assessment of trainees in the Responsible Conduct of Research and recent findings from the National Science Foundation Office of Inspector General regarding plagiarism suggests otherwise. Our experiences at a land-grant academic institution in assisting researchers in avoiding plagiarism are described. We provide evidence from a university-wide multi-disciplinary course that understanding how to avoid plagiarism in scientific writing is more difficult than it might appear, and that a failure to learn the rules of appropriate citation may cause dire consequences. We suggest that new strategies to provide training in avoiding plagiarism are required.

  16. Teachers' perception of the European scientists

    Directory of Open Access Journals (Sweden)

    Daniele Gouthier

    2007-09-01

    Full Text Available The first step of the SEDEC project has been a survey on teachers and pupils perception of science, scientists, and the European dimension of science. Different research actions have been organized for the different targets, and have been held in the six countries involved in the project: Czech Republic, France, Italy, Portugal, Poland and Romania. This article will present the results of a questionnaire distributed between European teachers. A research on the scientific imagery should have an opposite perspective to the one of a teacher at school; whereas the latter, the keeper of a knowledge, has the usual task of transferring and checking the knowledge in their students, a researcher has to record and describe their interior world relating to science – the information, but especially the images, the expectations, the emotions related to it.

  17. Communicating Ecology Through Art: What Scientists Think

    Directory of Open Access Journals (Sweden)

    David J. Curtis

    2012-06-01

    Full Text Available Many environmental issues facing society demand considerable public investment to reverse. However, this investment will only arise if the general community is supportive, and community support is only likely if the issues are widely understood. Scientists often find it difficult to communicate with the general public. The role of the visual and performing arts is often overlooked in this regard, yet the arts have long communicated issues, influenced and educated people, and challenged dominant paradigms. To assess the response of professional ecologists to the role of the arts in communicating science, a series of constructed performances and exhibitions was integrated into the program of a national ecological conference over five days. At the conclusion of the conference, responses were sought from the assembled scientists and research students toward using the arts for expanding audiences to ecological science. Over half the delegates said that elements of the arts program provided a conducive atmosphere for receiving information, encouraged them to reflect on alternative ways to communicate science, and persuaded them that the arts have a role in helping people understand complex scientific concepts. A sizeable minority of delegates (24% said they would consider incorporating the arts in their extension or outreach efforts. Incorporating music, theatre, and dance into a scientific conference can have many effects on participants and audiences. The arts can synthesize and convey complex scientific information, promote new ways of looking at issues, touch people's emotions, and create a celebratory atmosphere, as was evident in this case study. In like manner, the visual and performing arts should be harnessed to help extend the increasingly unpalatable and urgent messages of global climate change science to a lay audience worldwide.

  18. An example of woman scientist in France

    Science.gov (United States)

    Cazenave, A.

    2002-12-01

    Although the presence of women in sciences has been increasing in the past few decades in Europe, it remains incredibly low at the top levels. Recent statistics from the European Commission indicate that now women represent 50 per cent of first degree students in many countries. However, the proportion of women at each stage of the scientific career decreases almost linearly, reaching less than 10 per cent at the highest level jobs. From my own experience, I don't think that this results from sexism nor discrimination. Rather, I think that this is a result of complex cultural factors making women subconsciously persuaded that top level jobs are destined to male scientists only. Many women scientists drop the idea of playing a role at high-level research, considering it is a way of exerting power (a matter reserved to men). Others give up the possibility of combining childcare and high level commitments in research. And too many (married women) still find only natural to sacrifice their own scientific ambitions to the benefit of their spouse's career. In this poster, I briefly present my personal experience. I chose to prioritize scientific productivity and expertise versus hierarchical responsibilities. Besides I tried to keep a satisfactory balance between family demand and research involvement. This was indeed facilitated by the French system, which provides substantial support to women's work (nurseries, recreation centers during school holidays, etc.). To my point of view, the most promising way of increasing the number of women at top levels in research is through education and mentality evolution

  19. History and Outcomes of 50 Years of Physician-Scientist Training in Medical Scientist Training Programs.

    Science.gov (United States)

    Harding, Clifford V; Akabas, Myles H; Andersen, Olaf S

    2017-10-01

    Physician-scientists are needed to continue the great pace of recent biomedical research and translate scientific findings to clinical applications. MD-PhD programs represent one approach to train physician-scientists. MD-PhD training started in the 1950s and expanded greatly with the Medical Scientist Training Program (MSTP), launched in 1964 by the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health. MD-PhD training has been influenced by substantial changes in medical education, science, and clinical fields since its inception. In 2014, NIGMS held a 50th Anniversary MSTP Symposium highlighting the program and assessing its outcomes. In 2016, there were over 90 active MD-PhD programs in the United States, of which 45 were MSTP supported, with a total of 988 trainee slots. Over 10,000 students have received MSTP support since 1964. The authors present data for the demographic characteristics and outcomes for 9,683 MSTP trainees from 1975-2014. The integration of MD and PhD training has allowed trainees to develop a rigorous foundation in research in concert with clinical training. MSTP graduates have had relative success in obtaining research grants and have become prominent leaders in many biomedical research fields. Many challenges remain, however, including the need to maintain rigorous scientific components in evolving medical curricula, to enhance research-oriented residency and fellowship opportunities in a widening scope of fields targeted by MSTP graduates, to achieve greater racial diversity and gender balance in the physician-scientist workforce, and to sustain subsequent research activities of physician-scientists.

  20. Building the Next Generation of Earth Scientists: the Deep Carbon Observatory Early Career Scientist Workshops

    Science.gov (United States)

    Pratt, K.; Fellowes, J.; Giovannelli, D.; Stagno, V.

    2016-12-01

    Building a network of collaborators and colleagues is a key professional development activity for early career scientists (ECS) dealing with a challenging job market. At large conferences, young scientists often focus on interacting with senior researchers, competing for a small number of positions in leading laboratories. However, building a strong, international network amongst their peers in related disciplines is often as valuable in the long run. The Deep Carbon Observatory (DCO) began funding a series of workshops in 2014 designed to connect early career researchers within its extensive network of multidisciplinary scientists. The workshops, by design, are by and for early career scientists, thus removing any element of competition and focusing on peer-to-peer networking, collaboration, and creativity. The successful workshops, organized by committees of early career deep carbon scientists, have nucleated a lively community of like-minded individuals from around the world. Indeed, the organizers themselves often benefit greatly from the leadership experience of pulling together an international workshop on budget and on deadline. We have found that a combination of presentations from all participants in classroom sessions, professional development training such as communication and data management, and field-based relationship building and networking is a recipe for success. Small groups within the DCO ECS network have formed; publishing papers together, forging new research directions, and planning novel and ambitious field campaigns. Many DCO ECS also have come together to convene sessions at major international conferences, including the AGU Fall Meeting. Most of all, there is a broad sense of camaraderie and accessibility within the DCO ECS Community, providing the foundation for a career in the new, international, and interdisciplinary field of deep carbon science.

  1. Network Analysis of Beliefs About the Scientific Enterprise: A comparison of scientists, middle school science teachers and eighth-grade science students

    Science.gov (United States)

    Peters-Burton, Erin; Baynard, Liz R.

    2013-11-01

    An understanding of the scientific enterprise is useful because citizens need to make systematic, rational decisions about projects involving scientific endeavors and technology, and a clearer understanding of scientific epistemology is beneficial because it could encourage more public engagement with science. The purpose of this study was to capture beliefs for three groups, scientists, secondary science teachers, and eighth-grade science students, about the ways scientific knowledge is generated and validated. Open-ended questions were framed by formal scientific epistemology and dimensions of epistemology recognized in the field of educational psychology. The resulting statements were placed in a card sort and mapped in a network analysis to communicate interconnections among ideas. Maps analyzed with multidimensional scaling revealed robust connections among students and scientists but not among teachers. Student and teacher maps illustrated the strongest connections among ideas about experiments while scientist maps present more descriptive and well-rounded ideas about the scientific enterprise. The students' map was robust in terms of numbers of ideas, but were lacking in a hierarchical organization of ideas. The teachers' map displayed an alignment with the learning standards of the state, but not a broader view of science. The scientists map displayed a hierarchy of ideas with elaboration of equally valued statements connected to several foundational statements. Network analysis can be helpful in forwarding the study of views of the nature of science because of the technique's ability to capture verbatim statements from participants and to display the strength of connections among the statements.

  2. Differentially methylated DNA regions in monozygotic twin pairs discordant for rheumatoid arthritis.An epigenome - wide study.

    Directory of Open Access Journals (Sweden)

    Anders Jørgen Svendsen

    2016-11-01

    Full Text Available Objectives: In an explorative epigenome-wide association study (EWAS to search for gene independent, differentially methylated DNA positions (DMPs and regions (DMRs associated with rheumatoid arthritis (RA by studying monozygotic (MZ twin pairs discordant for rheumatoid arthritis.Methods: Genomic DNA was isolated from whole blood samples from 28 monozygotic (MZ twin pairs discordant for RA. DNA methylation was measured using the HumanMethylation450 BeadChips. Smoking, anti-cyclic citrullinated peptide antibodies and immunosuppressive treatment were included as covariates. Pathway analysis was performed using GREAT.Results: Smoking was significantly associated with hypomethylation of a DMR overlapping the promoter region of the RNF5 and the AGPAT1, which are implicated in inflammation and autoimmunity, whereas DMARD treatment induced hypermethylation of the same region. Additionally, the promotor region of both S100A6 and EFCAB4B were hypomethylated and both genes have previously been associated with RA. We replicated several candidate genes identified in a previous EWAS in treatment naïve RA singletons. Gene set analysis indicated the involvement of immunologic signatures and cancer-related pathways in RA.Conclusion: We identified several differentially methylated regions associated with RA which may represent environmental effects or consequences of the disease and plausible biological pathways pertinent to the pathogenesis of rheumatoid arthritis

  3. Genome-wide analysis of epigenomic alterations in fetal mouse forebrain after exposure to low doses of bisphenol A.

    Science.gov (United States)

    Yaoi, Takeshi; Itoh, Kyoko; Nakamura, Keiko; Ogi, Hiroshi; Fujiwara, Yasuhiro; Fushiki, Shinji

    2008-11-21

    Bisphenol A (BPA) is one of endocrine disrupting chemicals, being distributed widely in the environment. We have been studying the low dose effects of BPA on murine forebrain development. Here, we have investigated the genome-wide effect of maternal exposure to BPA on the epigenome in mouse forebrain at E12.5 and at E14.5. We scanned CpG methylation status in 2500 NotI loci, representing 48 (de)methylated unique loci. Methylation status in most of them was primarily developmental stage-dependent. Each of almost all cloned NotI loci was located in a CpG island (CGI) adjacent to 5' end of the transcriptional unit. The mRNA expression of two functionally related genes changed with development as well as the exposure to BPA. In both genes, changes at the transcriptional level correlated well with the changes in NotI methylation status. Taken together, epigenetic alterations in promoter-associated CGIs after exposure to BPA may underlie some effects on brain development.

  4. Ploidy-dependent changes in the epigenome of symbiotic cells correlate with specific patterns of gene expression

    KAUST Repository

    Nagymihály, Marianna

    2017-04-13

    The formation of symbiotic nodule cells in Medicago truncatula is driven by successive endoreduplication cycles and transcriptional reprogramming in different temporal waves including the activation of more than 600 cysteine-rich NCR genes expressed only in nodules. We show here that the transcriptional waves correlate with growing ploidy levels and have investigated how the epigenome changes during endoreduplication cycles. Differential DNA methylation was found in only a small subset of symbiotic nodule-specific genes, including more than half of the NCR genes, whereas in most genes DNA methylation was unaffected by the ploidy levels and was independent of the genes\\' active or repressed state. On the other hand, expression of nodule-specific genes correlated with ploidy-dependent opening of the chromatin as well as, in a subset of tested genes, with reduced H3K27me3 levels combined with enhanced H3K9ac levels. Our results suggest that endoreduplication-dependent epigenetic changes contribute to transcriptional reprogramming in the differentiation of symbiotic cells.

  5. Genomics and epigenomics in rheumatic diseases: what do they provide in terms of diagnosis and disease management?

    Science.gov (United States)

    Castro-Santos, Patricia; Díaz-Peña, Roberto

    2017-09-01

    Most rheumatic diseases are complex or multifactorial entities with pathogeneses that interact with both multiple genetic factors and a high number of diverse environmental factors. Knowledge of the human genome sequence and its diversity among populations has provided a crucial step forward in our understanding of genetic diseases, identifying many genetic loci or genes associated with diverse phenotypes. In general, susceptibility to autoimmunity is associated with multiple risk factors, but the mechanism of the environmental component influence is poorly understood. Studies in twins have demonstrated that genetics do not explain the totality of the pathogenesis of rheumatic diseases. One method of modulating gene expression through environmental effects is via epigenetic modifications. These techniques open a new field for identifying useful new biomarkers and therapeutic targets. In this context, the development of "-omics" techniques is an opportunity to progress in our knowledge of complex diseases, impacting the discovery of new potential biomarkers suitable for their introduction into clinical practice. In this review, we focus on the recent advances in the fields of genomics and epigenomics in rheumatic diseases and their potential to be useful for the diagnosis, follow-up, and treatment of these diseases. The ultimate aim of genomic studies in any human disease is to understand its pathogenesis, thereby enabling the prediction of the evolution of the disease to establish new treatments and address the development of personalized therapies.

  6. Who trusts scientists for information about climate change? Nuclear power? Vaccines?

    Science.gov (United States)

    Hamilton, L.

    2015-12-01

    US public acceptance/rejection of science on the topic of climate change has become highly polarized, with a demographic profile well established through survey research. Trust in scientists for information about climate change tends to increase with education, decrease with age, and is higher among self-identified liberals and moderates than among conservatives. Demographic profiles of people who do or do not trust scientists regarding other disputed topics are less well established. Some observers have argued that certain domains such as vaccines, nuclear power or genetically modified organisms (GMOs) could present a mirror image of climate change, with liberals instead of conservatives disproportionately rejecting science on that topic. Evidence for this mirror-image hypothesis has been mainly anecdotal, however. Here we test it systematically using statewide survey data on more than 1200 interviews, comparing five similarly worded questions that ask respondents whether they trust, don't trust, or are unsure about scientists as a source of information about ... climate change, vaccines, evolution, nuclear power safety, or GMOs. Climate change proves to be the most polarized of these topics, but all five exhibit roughly similar age, education and ideological effects -- contrary to the mirror-image hypothesis. The common patterns across five science domains, chosen for their hypothetical contrasts, map out an unexpectedly cohesive picture of who trusts scientists for information, and who does not. Implications of these survey results for public outreach and science communication are explored.

  7. Scientist Spotlight Homework Assignments Shift Students’ Stereotypes of Scientists and Enhance Science Identity in a Diverse Introductory Science Class

    Science.gov (United States)

    Schinske, Jeffrey N.; Perkins, Heather; Snyder, Amanda; Wyer, Mary

    2016-01-01

    Research into science identity, stereotype threat, and possible selves suggests a lack of diverse representations of scientists could impede traditionally underserved students from persisting and succeeding in science. We evaluated a series of metacognitive homework assignments (“Scientist Spotlights”) that featured counterstereotypical examples of scientists in an introductory biology class at a diverse community college. Scientist Spotlights additionally served as tools for content coverage, as scientists were selected to match topics covered each week. We analyzed beginning- and end-of-course essays completed by students during each of five courses with Scientist Spotlights and two courses with equivalent homework assignments that lacked connections to the stories of diverse scientists. Students completing Scientist Spotlights shifted toward counterstereotypical descriptions of scientists and conveyed an enhanced ability to personally relate to scientists following the intervention. Longitudinal data suggested these shifts were maintained 6 months after the completion of the course. Analyses further uncovered correlations between these shifts, interest in science, and course grades. As Scientist Spotlights require very little class time and complement existing curricula, they represent a promising tool for enhancing science identity, shifting stereotypes, and connecting content to issues of equity and diversity in a broad range of STEM classrooms. PMID:27587856

  8. Supervising Scientist, Annual Report 2000-2001

    International Nuclear Information System (INIS)

    2001-01-01

    The year under review has seen the resolution of the major issue that has dominated the work of the Supervising Scientist Division over the past three years the review of scientific uncertainties associated with the environmental assessment of the proposal to mine uranium at Jabiluka. The Supervising Scientist prepared a comprehensive report on the risks associated with mining at Jabiluka, which has been under various stages of peer review by an Independent Science Panel (ISP) appointed by the WHC since May 1999. This process culminated in a visit to Australia by the ISP in July 2000 for detailed discussion and assessment and the submission of the final report of the ISP to the World Heritage Committee in September 2000. The report of the ISP was considered at the meeting of the World Heritage Committee in Cairns in December 2000. The Committee reached the conclusion that 'the currently approved proposal for the mine and mill at Jabiluka does not threaten the health of people or the biological and ecological systems of Kakadu National Park that the Mission believed to be at risk'. As a result, the WHC decided not to register Kakadu National Park on the World Heritage List in Danger. But the people of Kakadu themselves remain to be convinced. A major challenge is to gain the confidence of Aboriginal people in the integrity and independence of our scientific assessments and to reduce the concerns that they have for the future of their people and their country. Monitoring of the Jabiluka project was extensive throughout the reporting period. Chemical and biological monitoring programmes of Energy Resources of Australia (ERA) and the Environmental Research Institute of the Supervising Scientist (ERISS) demonstrated that no adverse impact occurred in downstream aquatic ecosystems. Similarly, radiological measurements close to the nearest population centre demonstrated that radiation exposure of the public due to current operations at Jabiluka is not detectable

  9. Expanding Horizons Teachers and Scientists Collabortaing

    Science.gov (United States)

    Teres, A.

    2017-12-01

    As a participant in PolarTrec, I joined the crew of NASA's Operation IceBridge in Greenland for the month of April 2017. As an active member of the team I learned the ins and outs of field research, and I learned about the work done by Operation IceBridge. As a result of participating in this project, I grew as a teacher and a scientist. I took my experiences and shared them with my classroom through stories, pictures, videos, and my lesson plans. By seeing the Artic through my experiences the class became enraptured by the subject matter. I was no longer talking about a distant or abstract place instead I was talking about an experience. This enabled my students to take an active part in the discussion and to feel like the cryosphere was part of their life too. Not only did I learn about the science but I leaned about logistics of field research. I reached out to my community and local communications outlets before and after my trip to Greenland to familiarize whomever I could connect with about my experience. I contacted a local news station and they did an interview with me about my trip. I emailed a local newspaper about my trip and was interviewed before I left and after I returned. Due to the newscast, I was contacted by my college sorority and was interviewed for the sorority's national newsletter which is distributed throughout the United States. Each connection helped to spread the word. I'm continuing to spread the word by volunteering to present my experience to schools throughout Broward County in Florida. I've already connected with teachers and schools to set up my presentation in the calendar. Having these types of experiences is critical for teachers to continue their growth within the scientific field and education. Effective teachers are those not constrained by the walls of their classroom. Having the opportunity to work with scientists and do research in the field has expanded my horizons. The people I met I am still in contact with and I am

  10. Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple.

    Science.gov (United States)

    Xu, Jidi; Zhou, Shasha; Gong, Xiaoqing; Song, Yi; van Nocker, Steve; Ma, Fengwang; Guan, Qingmei

    2018-02-01

    Cytosine methylation is an essential feature of epigenetic regulation and is involved in various biological processes. Although cytosine methylation has been analysed at the genomic scale for several plant species, there is a general lack of understanding of the dynamics of global and genic DNA methylation in plants growing in environments challenged with biotic and abiotic stresses. In this study, we mapped cytosine methylation at single-base resolution in the genome of commercial apple (Malus x domestica), and analysed changes in methylation patterns associated with water deficit in representative drought-sensitive and drought-tolerant cultivars. We found that the apple genome exhibits ~54%, ~38% and ~8.5% methylation at CG, CHG and CHH sequence contexts, respectively. We additionally documented changes in gene expression associated with water deficit in an attempt to link methylation and gene expression changes. Global methylation and transcription analysis revealed that promoter-unmethylated genes showed higher expression levels than promoter-methylated genes. Gene body methylation appears to be positively correlated with gene expression. Water deficit stress was associated with changes in methylation at a multitude of genes, including those encoding transcription factors (TFs) and transposable elements (TEs). These results present a methylome map of the apple genome and reveal widespread DNA methylation alterations in response to water deficit stress. These data will be helpful for understanding potential linkages between DNA methylation and gene expression in plants growing in natural environments and challenged with abiotic and biotic stresses. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  11. Construction of barley consensus map showing chromosomal ...

    African Journals Online (AJOL)

    GRACE

    2006-02-02

    Feb 2, 2006 ... the purpose of this consensus map (containing QTL) is to provide a tool for scientists to accurately locate molecular markers to ... community with powerful tools for comparative genomics. (Gai et al., 2000; Mekhdov et al., ...... and controlled by almost the same loci (Marquez et al.,. 2000). In the present study ...

  12. The first scientist Anaximander and his legacy

    CERN Document Server

    Rovelli, Carlo

    2011-01-01

    Carlo Rovelli, a leading theoretical physicist, uses the figure of Anaximander as the starting point for an examination of scientific thinking itself: its limits, its strengths, its benefits to humankind, and its controversial relationship with religion. Anaximander, the sixth-century BC Greek philosopher, is often called the first scientist because he was the first to explain that order in the world was due to natural forces, not supernatural ones. He is the first person known to rnunderstand that the Earth floats in space; to believe that the sun, the moon, and the stars rotate around it--seven centuries before Ptolemy; to argue that all animals came from the sea and evolved; and to posit that universal laws rncontrol all change in the world. Anaximander taught Pythagoras, who would build on Anaximander's scientific theories by applying mathematical laws to natural phenomena. rnrnIn the award-winning Anaximander and the Birth of Scientific Thought, Rovelli restores Anaximander to his place in the history of...

  13. Scientists' views about attribution of global warming.

    Science.gov (United States)

    Verheggen, Bart; Strengers, Bart; Cook, John; van Dorland, Rob; Vringer, Kees; Peters, Jeroen; Visser, Hans; Meyer, Leo

    2014-08-19

    Results are presented from a survey held among 1868 scientists studying various aspects of climate change, including physical climate, climate impacts, and mitigation. The survey was unique in its size, broadness and level of detail. Consistent with other research, we found that, as the level of expertise in climate science grew, so too did the level of agreement on anthropogenic causation. 90% of respondents with more than 10 climate-related peer-reviewed publications (about half of all respondents), explicitly agreed with anthropogenic greenhouse gases (GHGs) being the dominant driver of recent global warming. The respondents' quantitative estimate of the GHG contribution appeared to strongly depend on their judgment or knowledge of the cooling effect of aerosols. The phrasing of the IPCC attribution statement in its fourth assessment report (AR4)-providing a lower limit for the isolated GHG contribution-may have led to an underestimation of the GHG influence on recent warming. The phrasing was improved in AR5. We also report on the respondents' views on other factors contributing to global warming; of these Land Use and Land Cover Change (LULCC) was considered the most important. Respondents who characterized human influence on climate as insignificant, reported having had the most frequent media coverage regarding their views on climate change.

  14. Cell Scientist to Watch - Jacky Goetz.

    Science.gov (United States)

    2017-07-01

    Jacky Goetz graduated in pharmacology and cell biology from the University of Strasbourg in France and moved to Canada to the laboratory of Ivan Robert Nabi at the University of Montreal and later the University of British Columbia, to work on the interaction between the endoplasmic reticulum and mitochondria, as well as the glycosylation of membrane proteins. In 2007, he received his PhD from both the University of Montreal and the University of Strasbourg. For his postdoc, Jacky moved to the Spanish national centre for cardiovascular research (CNIC) in Madrid and the laboratory of Miguel Angel del Pozo to study the tumour microenvironment. Subsequently, Jacky joined the laboratory of Julien Vermot at the Institute of Genetics and Molecular and Cellular Biology (IGBMC) in Strasbourg to pursue his interests in mechanotransduction. In 2012, he won the French Society for Cell Biology (SBCF) Young Scientist Award and, in 2013, he started his own research group - 'Tumor Biomechanics' - in Strasbourg to work on intravital imaging methods and biomechanical forces during tumour progression. © 2017. Published by The Company of Biologists Ltd.

  15. Scientists present their design for Einstein Telescope

    CERN Multimedia

    ASPERA Press Release

    2011-01-01

    Plans shape up for a revolutionary new observatory that will explore black holes and the Big Bang. This detector will ‘see’ the Universe in gravitational waves.   A new era in astronomy will come a step closer when scientists from across Europe present their design study today for an advanced observatory capable of making precision measurements of gravitational waves – minute ripples in the fabric of spacetime – predicted to emanate from cosmic catastrophes such as merging black holes and collapsing stars and supernovae. It also offers the potential to probe the earliest moments of the Universe just after the Big Bang, which are currently inaccessible. The Einstein Observatory (ET) is a so-called third-generation gravitational-wave (GW) detector, which will be 100 times more sensitive than current instruments. Like the first two generations of GW detectors, it is based on the measurement of tiny changes (far less than the size of an atomic nucleus) in the le...

  16. Astronaut Kevin Chilton displays map of Scandinavia on flight deck

    Science.gov (United States)

    1994-01-01

    Astronaut Kevin P. Chilton, pilot, displays a map of Scandinavia on the Space Shuttle Endeavour's flight deck. Large scale maps such as this were used by the crew to locate specific sites of interest to the Space Radar Laboratory scientists. The crew then photographed the sites at the same time as the radar in the payload bay imaged them.

  17. Painting a picture across the landscape with ModelMap

    Science.gov (United States)

    Brian Cooke; Elizabeth Freeman; Gretchen Moisen; Tracey Frescino

    2017-01-01

    Scientists and statisticians working for the Rocky Mountain Research Station have created a software package that simplifies and automates many of the processes needed for converting models into maps. This software package, called ModelMap, has helped a variety of specialists and land managers to quickly convert data into easily understood graphical images. The...

  18. Causal mapping

    DEFF Research Database (Denmark)

    Rasmussen, Lauge Baungaard

    2006-01-01

    The lecture note explains how to use the causal mapping method as well as the theoretical framework aoosciated to the method......The lecture note explains how to use the causal mapping method as well as the theoretical framework aoosciated to the method...

  19. Collection Mapping.

    Science.gov (United States)

    Harbour, Denise

    2002-01-01

    Explains collection mapping for library media collections. Discusses purposes for creating collection maps, including helping with selection and weeding decisions, showing how the collection supports the curriculum, and making budget decisions; and methods of data collection, including evaluating a collaboratively taught unit with the classroom…

  20. CALS Mapping

    DEFF Research Database (Denmark)

    Collin, Ib; Nielsen, Povl Holm; Larsen, Michael Holm

    1998-01-01

    To enhance the industrial applications of CALS, CALS Center Danmark has developed a cost efficient and transparent assessment, CALS Mapping, to uncover the potential of CALS - primarily dedicated to small and medium sized enterprises. The idea behind CALS Mapping is that the CALS State of the ent...

  1. Scientists' understanding of public communication of science and technology

    DEFF Research Database (Denmark)

    Nielsen, Kristian Hvidtfelt; Kjaer, Carsten Rahbæk; Dahlgaard, Jørgen

    Background Research into the field of science communication has tended to focus on public understanding of science or on the processes of science communication itself, e.g. by looking at science in the media. Few studies have explored how scientists understand science communication. At present......, there seems to be two competing ways of framing the role of scientists in the process of science communication. The linear model stresses onedirectional flow of knowledge from scientists to the general public whereas the interactional, reflective model emphasizes dialogue and upstream engagement. Recent...... British studies of scientists' opinions on science communication have shown that most scientists operate in the framework of the linear model. However, public and government pressure to increase scientists' exchange of knowledge and competencies with society may be changing this perception. Objective...

  2. Description of Nurse Scientists in a Large Health Care System.

    Science.gov (United States)

    Logsdon, M Cynthia; Kleiner, Catherine; Oster, Cynthia A; Smith, Claudia DiSabatino; Bergman-Evans, Brenda; Kempnich, Jodeena M; Hogan, Felicia; Myers, John

    Replicating a research study that described the work of nurse scientists in children's hospitals, the purpose of the study was to describe the role, activities, and outcomes of nurse scientists employed in a national health care organization. The characteristics of nurses filling the nurse scientist role in clinical settings and outcomes associated with the role have not been extensively described. The setting of this study is ideal since the organization includes facilities of various sizes located in rural, urban, and suburban areas in 18 states. Names and contact information of nurse scientists were obtained from nurse executives at each of the 110 affiliated organizations. Nurse scientists completed an anonymous survey. The primary role of the nurse scientists is to facilitate the work of others. Recommendations to strengthen the research infrastructure are provided.

  3. Scientists' Prioritization of Communication Objectives for Public Engagement.

    Science.gov (United States)

    Dudo, Anthony; Besley, John C

    2016-01-01

    Amid calls from scientific leaders for their colleagues to become more effective public communicators, this study examines the objectives that scientists' report drive their public engagement behaviors. We explore how scientists evaluate five specific communication objectives, which include informing the public about science, exciting the public about science, strengthening the public's trust in science, tailoring messages about science, and defending science from misinformation. We use insights from extant research, the theory of planned behavior, and procedural justice theory to identify likely predictors of scientists' views about these communication objectives. Results show that scientists most prioritize communication designed to defend science from misinformation and educate the public about science, and least prioritize communication that seeks to build trust and establish resonance with the public. Regression analyses reveal factors associated with scientists who prioritize each of the five specific communication objectives. Our findings highlight the need for communication trainers to help scientists select specific communication objectives for particular contexts and audiences.

  4. The physician-scientists: rare species in Africa.

    Science.gov (United States)

    Adefuye, Anthonio Oladele; Adeola, Henry Ademola; Bezuidenhout, Johan

    2018-01-01

    There is paucity of physician-scientists in Africa, resulting in overt dependence of clinical practice on research findings from advanced "first world" countries. Physician-scientists include individuals with a medical degree alone or combined with other advanced degrees (e.g. MD/MBChB and PhD) with a career path in biomedical/ translational and patient-oriented/evaluative science research. The paucity of clinically trained research scientists in Africa could result in dire consequences as exemplified in the recent Ebola virus epidemic in West Africa, where shortage of skilled clinical scientists, played a major role in disease progression and mortality. Here we contextualise the role of physician-scientist in health care management, highlight factors limiting the training of physician-scientist in Africa and proffer implementable recommendations to address these factors.

  5. Scientists and software engineers: A tale of two cultures

    OpenAIRE

    Segal, Judith

    2008-01-01

    The two cultures of the title are those observed in my field studies: the culture of scientists (financial\\ud mathematicians, earth and planetary scientists, and molecular biologists) developing their own software, and the culture of software engineers developing scientific software. In this paper, I shall describe some problems arising when scientists and software engineers come together to develop scientific software and discuss how these problems may be ascribed to their two different cult...

  6. Association of Polar Early Career Scientists Promotes Professional Skills

    Science.gov (United States)

    Pope, Allen; Fugmann, Gerlis; Kruse, Frigga

    2014-06-01

    As a partner organization of AGU, the Association of Polar Early Career Scientists (APECS; http://www.apecs.is) fully supports the views expressed in Wendy Gordon's Forum article "Developing Scientists' `Soft' Skills" (Eos, 95(6), 55, doi:10.1002/2014EO060003). Her recognition that beyond research skills, people skills and professional training are crucial to the success of any early-career scientist is encouraging.

  7. Investigation of the Secondary School Students’ Images of Scientists

    OpenAIRE

    Akgün, Abuzer

    2016-01-01

    The overall purpose of this study is to explore secondary school students’ images of scientists. In addition to this comprehensive purpose, it is also investigated that if these students’ current images of scientists and those in which they see themselves as a scientist in the near future are consistent or not. The study was designed in line with the case study research in a qualitatively manner. The working group is of totally 175 (95 boys, 81 girls) secondary school students enrolled in the...

  8. Making open data work for plant scientists.

    Science.gov (United States)

    Leonelli, Sabina; Smirnoff, Nicholas; Moore, Jonathan; Cook, Charis; Bastow, Ruth

    2013-11-01

    Despite the clear demand for open data sharing, its implementation within plant science is still limited. This is, at least in part, because open data-sharing raises several unanswered questions and challenges to current research practices. In this commentary, some of the challenges encountered by plant researchers at the bench when generating, interpreting, and attempting to disseminate their data have been highlighted. The difficulties involved in sharing sequencing, transcriptomics, proteomics, and metabolomics data are reviewed. The benefits and drawbacks of three data-sharing venues currently available to plant scientists are identified and assessed: (i) journal publication; (ii) university repositories; and (iii) community and project-specific databases. It is concluded that community and project-specific databases are the most useful to researchers interested in effective data sharing, since these databases are explicitly created to meet the researchers' needs, support extensive curation, and embody a heightened awareness of what it takes to make data reuseable by others. Such bottom-up and community-driven approaches need to be valued by the research community, supported by publishers, and provided with long-term sustainable support by funding bodies and government. At the same time, these databases need to be linked to generic databases where possible, in order to be discoverable to the majority of researchers and thus promote effective and efficient data sharing. As we look forward to a future that embraces open access to data and publications, it is essential that data policies, data curation, data integration, data infrastructure, and data funding are linked together so as to foster data access and research productivity.

  9. Written Communication Skills for Scientists and Engineers

    Science.gov (United States)

    Narayanan, M.

    2016-12-01

    Lord Chancellor, Francis Bacon of England said: Reading maketh a full man; conference a ready man; and writing an exact man. Even after his death, Francis Bacon remained extremely influential through his works, especially as philosophical advocate and practitioner of the scientific method during the scientific revolution. Written communication skills are extremely important for scientists and engineers because it helps them to achieve their goals effectively and meet stipulated deadlines according to a pre-established schedule. Richard Arum and Josipa Roksa claim that American students are learning very little during their first two years of college (Arum and Roksa, 2011). Written communication involves expressing yourself clearly, using language with precision; constructing a logical argument; taking notes; editing and summarizing; and writing reports. There are three main elements to written communication. First and foremost is the structure because this in principle outlines clearly the way the entire content is laid out. Second, the style which primarily indicates the way it is written and how communication is made effective and vibrant. Third, the content which should document in complete detail, what you are writing about. Some researchers indicate that colleges and universities are failing to prepare the students to meet the demanding challenges of the present day workforce and are struggling to maintain an international status (Johnson, K. 2013). In this presentation, the author provides some guidelines to help students improve their written communication skills. References: Johnson, Kristine (2013) "Why Students Don't Write: Educating in the Era of Credentialing: Academically Adrift: Limited Learning on College Campuses," Conversations on Jesuit Higher Education: Vol. 43, Article 9. Available at: http://epublications.marquette.edu/conversations/vol43/iss1/9 Arum, Richard and Roksa, Josipa (2011) Academically Adrift: Limited Learning on College Campuses

  10. Flow Cytometry Scientist | Center for Cancer Research

    Science.gov (United States)

    The Basic Science Program (BSP) pursues independent, multidisciplinary research in basic and applied molecular biology, immunology, retrovirology, cancer biology, and human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick National Laboratory for Cancer Research (FNLCR). KEY ROLES/RESPONSIBILITIES The Flow Cytometry Core (Flow Core) in the Cancer and Inflammation Program (CIP) is a service core which supports the research efforts of the CCR by providing expertise in the field of flow cytometry (fluorescence cell sorting) with the goal of gaining a more thorough understanding of the biology of the immune system, cancer, and inflammation processes. The Flow Core provides service to 12-15 CIP laboratories and more than 22 non-CIP laboratories. Flow core staff provide technical advice on the experimental design of applications, which include immunological phenotyping, cell function assays, and cell cycle analysis. Work is performed per customer requirements, and no independent research is involved. Flow Cytometry Scientist - The individual will be responsible for: Daily management of the Flow Cytometry Core, to include the supervision and guidance of technical staff members Monitor performance of and maintain high-dimensional flow cytometer analyzers and cell sorters Operate high-dimensional flow cytometer analyzers and cell sorters Provide scientific expertise to the user community and facilitate the development of cutting-edge technologies Interact with Flow Core users and customers, and provide technical and scientific advice, and guidance regarding their experiments, including possible collaborations Train staff and scientific end users on the use of flow cytometry in their research, as well as teach them how to operate and troubleshoot the bench-top analyzer instruments Prepare and deliver lectures, as well as one-on-one training sessions, with customers/users Ensure that protocols are up

  11. Science Enhancements by the MAVEN Participating Scientists

    Science.gov (United States)

    Grebowsky, J.; Fast, K.; Talaat, E.; Combi, M.; Crary, F.; England, S.; Ma, Y.; Mendillo, M.; Rosenblatt, P.; Seki, K.

    2014-01-01

    NASA implemented a Participating Scientist Program and released a solicitation for the Mars Atmosphere and Volatile EvolutioN mission (MAVEN) proposals on February 14, 2013. After a NASA peer review panel evaluated the proposals, NASA Headquarters selected nine on June 12, 2013. The program's intent is to enhance the science return from the mission by including new investigations that broaden and/or complement the baseline investigations, while still addressing key science goals. The selections cover a broad range of science investigations. Included are: a patching of a 3D exosphere model to an improved global ionosphere-thermosphere model to study the generation of the exosphere and calculate the escape rates; the addition of a focused study of upper atmosphere variability and waves; improvement of a multi-fluid magnetohydrodynamic model that will be adjusted according to MAVEN observations to enhance the understanding of the solar-wind plasma interaction; a global study of the state of the ionosphere; folding MAVEN measurements into the Mars International Reference Ionosphere under development; quantification of atmospheric loss by pick-up using ion cyclotron wave observations; the reconciliation of remote and in situ observations of the upper atmosphere; the application of precise orbit determination of the spacecraft to measure upper atmospheric density and in conjunction with other Mars missions improve the static gravity field model of Mars; and an integrated ion/neutral study of ionospheric flows and resultant heavy ion escape. Descriptions of each of these investigations are given showing how each adds to and fits seamlessly into MAVEN mission science design.

  12. Thermodynamics for physicists, chemists and materials scientists

    CERN Document Server

    Hentschke, Reinhard

    2014-01-01

    Thermodynamics is the foundation of many-body physics and thus of physical chemistry and material science as well. Today new sources of useful energy, energy storage, transport and conversion, requiring development of novel technology, are of rapidly increasing importance. This development strongly affects modern industry. Thus thermodynamics will have to be given more prominence in the science curriculum in colleges and universities - something that is attempted in this book. The structure of this text is simple and transparent, enabling the easy mapping of the text onto a one-semester course syllabus and the attendant study. There are 8 chapters total and one three-part appendix. Throughout the text the student finds numerous examples (solved problems) reaching from cosmic to molecular evolution or from cloud formation to Bose condensation.

  13. Epigenome-wide study for the offspring exposed to maternal HBV infection during pregnancy, a pilot study.

    Science.gov (United States)

    Cheng, Qijun; Zhao, Bin; Huang, Zhenxiang; Su, Yanhua; Chen, Biqin; Yang, Songjing; Peng, Xueqi; Ma, Qilin; Yu, Xiaoshan; Zhao, Benhua; Ke, Xiayi

    2018-06-05

    Hepatitis B virus (HBV) can be transmitted to infants, and is related to infants' later disease risk. Epigenetic change (such as DNA methylation) may be mechanism underlying the relationship. In this study, we aimed to investigate whether prenatal HBV infection could alter DNA methylation status in newborns. We selected 12 neonates with intrauterine HBV infection whose mothers were HBsAg-positive during pregnancy, relative to 12 HBV-free neonates with HBsAg-negative mothers. The pattern of genome-wide DNA methylation in the umbilical cord blood was investigated by Illumina Infinium Human Methylation 450K BeadChip. The average level of global methylation in infected neonates exposed to maternal HBV infection was not significantly different from controls. However, after adjusting for multiple comparisons, we found differential significance in the cases group compared to the controls for 663 CpG sites, associated with 534 genes. Among these sites, 53.85% (357/663) had decreased methylation (ΔM  0). The average percentage change (Δβ) in methylation ranged from -46% to 36%. Validated by pyrosequencing, we identified 4 significantly differentially methylated CpG sites in the KLHL35 gene and additional CpGs for the CPT1B gene. These genes play a role in the development of hepatocellular and colorectal carcinoma and fatty acid oxidation, suggesting the candidature of these genes in HBV related disease. Prenatal HBV exposure, even without malformation or preterm birth, may alter the epigenome profile in newborns. We identified a set of genes with differentially methylated CpG sites presented in the cord blood of HBV-infected newborns with HBsAg-positive mothers, demonstrating that DNA methylation status at birth can be used as a biomarker of prenatal exposure. These DNA methylation differences suggest a possible role for epigenetic processes in neonatal development in response to prenatal HBV exposure. Copyright © 2018 Elsevier B.V. All rights reserved.

  14. Transcript levels of several epigenome regulatory genes in bovine somatic donor cells are not correlated with their cloning efficiency.

    Science.gov (United States)

    Zhou, Wenli; Sadeghieh, Sanaz; Abruzzese, Ronald; Uppada, Subhadra; Meredith, Justin; Ohlrichs, Charletta; Broek, Diane; Polejaeva, Irina

    2009-09-01

    Among many factors that potentially affect somatic cell nuclear transfer (SCNT) embryo development is the donor cell itself. Cloning potentials of somatic donor cells vary greatly, possibly because the cells have different capacities to be reprogrammed by ooplasma. It is therefore intriguing to identify factors that regulate the reprogrammability of somatic donor cells. Gene expression analysis is a widely used tool to investigate underlying mechanisms of various phenotypes. In this study, we conducted a retrospective analysis investigating whether donor cell lines with distinct cloning efficiencies express different levels of genes involved in epigenetic reprogramming including histone deacetylase-1 (HDAC1), -2 (HDAC2); DNA methyltransferase-1 (DNMT1), -3a (DNMT3a),-3b (DNMT3b), and the bovine homolog of yeast sucrose nonfermenting-2 (SNF2L), a SWI/SNF family of ATPases. Cell samples from 12 bovine donor cell lines were collected at the time of nuclear transfer experiments and expression levels of the genes were measured using quantitative polymerase chain reaction (PCR). Our results show that there are no significant differences in expression levels of these genes between donor cell lines of high and low cloning efficiency defined as live calving rates, although inverse correlations are observed between in vitro embryo developmental rates and expression levels of HDAC2 and SNF2L. We also show that selection of stable reference genes is important for relative quantification, and different batches of cells can have different gene expression patterns. In summary, we demonstrate that expression levels of these epigenome regulatory genes in bovine donor cells are not correlated with cloning potential. The experimental design and data analysis method reported here can be applied to study any genes expressed in donor cells.

  15. Correlation between desiccation stress response and epigenetic modifications of genes in Drosophila melanogaster: An example of environment-epigenome interaction.

    Science.gov (United States)

    Sharma, Vineeta; Kohli, Surbhi; Brahmachari, Vani

    2017-10-01

    Animals from different phyla including arthropods tolerate water stress to different extent. This tolerance is accompanied by biochemical changes which in turn are due to transcriptional alteration. The changes in transcription can be an indirect effect on some of the genes, ensuing from the effect of stress on the regulators of transcription including epigenetic regulators. Within this paradigm, we investigated the correlation between stress response and epigenetic modification underlying gene expression modulation during desiccation stress in Canton-S. We report altered resistance of flies in desiccation stress for heterozygote mutants of PcG and TrxG members. Pc/+ mutant shows lower survival, while ash1/+ mutants show higher survival under desiccation stress as compared to Canton-S. We detect expression alteration in stress related genes as well the genes of the Polycomb and trithorax complex in Canton-S subjected to desiccation stress. Concomitant with this, there is an altered enrichment of H3K27me3 and H3K4me3 at the upstream regions of the stress responsive genes. The enrichment of activating mark, H3K4me3, is higher in non-stress condition. H3K27me3, the repressive mark, is more pronounced under stress condition, which in turn, can be correlated with the binding of Pc. Our results show that desiccation stress induces dynamic switching in expression and enrichment of PcG and TrxG in the upstream region of genes, which correlates with histone modifications. We provide evidence that epigenetic modulation could be one of the mechanisms to adapt to the desiccation stress in Drosophila. Thus, our study proposes the interaction of epigenome and environmental factors. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Cortical Maps.

    Science.gov (United States)

    Bednar, James A; Wilson, Stuart P

    2016-12-01

    In this article, we review functional organization in sensory cortical regions-how the cortex represents the world. We consider four interrelated aspects of cortical organization: (1) the set of receptive fields of individual cortical sensory neurons, (2) how lateral interaction between cortical neurons reflects the similarity of their receptive fields, (3) the spatial distribution of receptive-field properties across the horizontal extent of the cortical tissue, and (4) how the spatial distributions of different receptive-field properties interact with one another. We show how these data are generally well explained by the theory of input-driven self-organization, with a family of computational models of cortical maps offering a parsimonious account for a wide range of map-related phenomena. We then discuss important challenges to this explanation, with respect to the maps present at birth, maps present under activity blockade, the limits of adult plasticity, and the lack of some maps in rodents. Because there is not at present another credible general theory for cortical map development, we conclude by proposing key experiments to help uncover other mechanisms that might also be operating during map development. © The Author(s) 2015.

  17. Access to scientific publications: the scientist's perspective.

    Science.gov (United States)

    Voronin, Yegor; Myrzahmetov, Askar; Bernstein, Alan

    2011-01-01

    research literature. Access to papers through subscriptions is complemented by a variety of other means, including emailing corresponding authors, joint affiliations, use of someone else's login information and posting requests on message boards. This complex picture makes it difficult to assess the real ability of scientists to access literature, but the observed differences in access levels between institutions suggest an unlevel playing field, in which some researchers have to spend more efforts than others to obtain the same information.

  18. Access to scientific publications: the scientist's perspective.

    Directory of Open Access Journals (Sweden)

    Yegor Voronin

    , subscriptions do not provide access to the full range of HIV vaccine research literature. Access to papers through subscriptions is complemented by a variety of other means, including emailing corresponding authors, joint affiliations, use of someone else's login information and posting requests on message boards. This complex picture makes it difficult to assess the real ability of scientists to access literature, but the observed differences in access levels between institutions suggest an unlevel playing field, in which some researchers have to spend more efforts than others to obtain the same information.

  19. Genetic Mapping

    Science.gov (United States)

    ... Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for Teachers Genomic ... genetic mapping? Among the main goals of the Human Genome Project (HGP) was to develop new, better and cheaper ...

  20. Affective Maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    . In particular, mapping environmental damage, endangered species, and human made disasters has become one of the focal point of affective knowledge production. These ‘more-than-humangeographies’ practices include notions of species, space and territory, and movement towards a new political ecology. This type...... of digital cartographies has been highlighted as the ‘processual turn’ in critical cartography, whereas in related computational journalism it can be seen as an interactive and iterative process of mapping complex and fragile ecological developments. This paper looks at computer-assisted cartography as part...... of environmental knowledge production. It uses InfoAmazonia, the databased platform on Amazon rainforests, as an example of affective geo-visualization within information mapping that enhances embodiment in the experience of the information. Amazonia is defined as a digitally created affective (map)space within...

  1. Of Science and Scientists an Anthology of Anecdotes

    Science.gov (United States)

    Kothare, A. N.

    Although a lot is available in the form of biographies and writings of scientists, very little information is found on what made them not only great discoverers but humane too, blessed with humour, humility and humanism. This book helps to convey this very aspect of scientists who while being involved in their unique adventure are like us, the lesser mortals.

  2. Russian scientists make desperate plea to save nuclear institute

    CERN Multimedia

    2003-01-01

    Scientists from a Russian nuclear research institute recently held a news conference in Moscow to publicize their work on a revolutionary new type of nuclear reactor. However, it transpired that the scientists were worried about their institute being closed down, and saw the news conference as an opportunity to draw attention to their plight (1 page).

  3. Continuous professional training of medical laboratory scientists in ...

    African Journals Online (AJOL)

    Background. Training and re-training of healthcare workers is pivotal to improved service delivery. Objective. To determine the proportion of practising medical laboratory scientists with in-service training in Benin City, Nigeria and areas covered by these programmes. Methods. Medical laboratory scientists from Benin City ...

  4. The Use of Internet by Academic Scientists in Modibbo Adama ...

    African Journals Online (AJOL)

    The internet is an important tool for communication and retrieval of information. This study examined the use of internet in communication and retrieval of information by scientists in Modibbo Adama University of Technology, Yola.The survey method was used for the study. A total of 95 scientists in the school of pure and ...

  5. Dorothy Crowfoot Hodgkin – A Tribute The word 'scientist' evokes ...

    Indian Academy of Sciences (India)

    milind1

    Then there is a current image of a scientist-manager raising large funds, filing patents, hopping from meeting to meeting, leading large teams and producing results of great import to science as well as industry. These or other images do not fit Dorothy Crowfoot Hodgkin. Undoubtedly, she was an outstanding scientist with.

  6. The medical laboratory scientist in the clinical chemistry service ...

    African Journals Online (AJOL)

    The recent opening of an official register for medicallaboratory scientists in South Africa has prompted an examination of the professional role, training and qualification of one particular group of scientists, namely clinical chemists working in hospital pathology departments. Lack of recognition of the potential contribution of ...

  7. Collaborating with Scientists in Education and Public Engagement

    Science.gov (United States)

    Shupla, C. B.; Shaner, A. J.; Hackler, A. S.

    2016-12-01

    The Education and Public Engagement team at the Lunar and Planetary Institute (LPI) is developing a scientific advisory board, to gather input from planetary scientists for ways that LPI can help them with public engagement (such as connecting them to opportunities, creating useful resources, and providing training). The advisory board will also assist in outlining possible roles of scientists in public engagement, provide feedback on LPI scientist engagement efforts, and encourage scientists to participate in various education and public engagement events. LPI's scientists have participated in a variety of education programs, including teacher workshops, family events, public presentations, informal educator trainings, and communication workshops. Scientists have helped conduct hands-on activities, participated in group discussions, and given talks, while sharing their own career paths and interests; these activities have provided audiences with a clearer vision of how science is conducted and how they can become engaged in science themselves. We will share the status and current findings of the scientist advisory board, and the resulting lessons learned regarding scientists' needs, abilities, and interests in participating in education and public engagement programs.

  8. Assessing the bibliometric productivity of forest scientists in Italy

    Directory of Open Access Journals (Sweden)

    Francesca Giannetti

    2016-07-01

    Full Text Available Since 2010, the Italian Ministry of University and Research issued new evaluation protocols to select candidates for University professorships and assess the bibliometric productivity of Universities and Research Institutes based on bibliometric indicators, i.e. scientific paper and citation numbers and the h-index. Under this framework, the objective of this study was to quantify the bibliometric productivity of the Italian forest research community during the 2002-2012 period. We examined the following productivity parameters: (i the bibliometric productivity under the Forestry subject category at the global level; (ii compared the aggregated bibliometric productivity of Italian forest scientists with scientists from other countries; (iii analyzed publication and citation temporal trends of Italian forest scientists and their international collaborations; and (iv characterized productivity distribution among Italian forest scientists at different career levels. Results indicated the following: (i the UK is the most efficient country based on the ratio between Gross Domestic Spending (GDS on Research and Development (R&D and bibliometric productivity under the Forestry subject category, followed by Italy; (ii Italian forest scientist productivity exhibited a significant positive time trend, but was characterized by high inequality across authors; (iii one-half of the Italian forest scientist publications were written in collaboration with foreign scientists; (iv a strong relationship exists between bibliometric indicators calculated by WOS and SCOPUS, suggesting these two databases have the same potential to evaluate the forestry research community; and (v self-citations did not significantly affect the rank of Italian forest scientists.

  9. Improved small stock production between scientist and producer ...

    African Journals Online (AJOL)

    small stock production involves close cooperation between the animal scientist and the producer. ... Presented at the Symposium on 'The scientist serving animal production' at the 25th Annual Congress of the .... This fact rendered the other type of abortion identified of very little practical significance. Further observations in ...

  10. The immoral landscape? Scientists are associated with violations of morality

    NARCIS (Netherlands)

    Rutjens, B.T.; Heine, S.J.

    2016-01-01

    Do people think that scientists are bad people? Although surveys find that science is a highly respected profession, a growing discourse has emerged regarding how science is often judged negatively. We report ten studies (N = 2328) that investigated morality judgments of scientists and compared

  11. Who believes in the storybook image of the scientist?

    NARCIS (Netherlands)

    Veldkamp, C.L S; Hartgerink, C.H.J.; van Assen, M.A.L.M.; Wicherts, J.M.

    2017-01-01

    Do lay people and scientists themselves recognize that scientists are human and therefore prone to human fallibilities such as error, bias, and even dishonesty? In a series of three experimental studies and one correlational study (total N = 3,278) we found that the 'storybook image of the

  12. Who Believes in the Storybook Image of the Scientist?

    NARCIS (Netherlands)

    Veldkamp, Coosje L S; Hartgerink, Chris H J; van Assen, Marcel A.L.M.; Wicherts, Jelte M.

    2017-01-01

    Do lay people and scientists themselves recognize that scientists are human and therefore prone to human fallibilities such as error, bias, and even dishonesty? In a series of three experimental studies and one correlational study (total N = 3,278) we found that the “storybook image of the

  13. Promoting Best Research Practices Amongst Palms Scientists in ...

    African Journals Online (AJOL)

    The aim of this paper is to investigate the level and reasons of plagiarism of literature among palm scientists in Nigeria. The questionnaire was adopted to gather data in this study. The questionnaire was administered by the researcher to scientists that have published at least one palm article. Usable data were collected ...

  14. Children's Images of Scientists: Does Grade Level Make a Difference?

    Science.gov (United States)

    Ozel, Murat

    2012-01-01

    The purpose of this study was to assess children's images of scientists by using the Draw-A-Scientist Test (DAST) and to determine if differences in these images exist between grade levels. The DAST was administered to 243 children who were enrolled in kindergarten (aged 6) and grade 3 and 5 (aged 9 and 11). Findings obtained from the study…

  15. The Media: The Image of the Scientist is Bad

    Science.gov (United States)

    Maugh, Thomas H., II

    1978-01-01

    Many individuals are concerned with the erroneous image of science and scientists that is given to the public by the media. To improve the situation, it is suggested that individuals and organizations protest to movie studios and networks when inaccuracies appear and when scientists are portrayed in a denigrating manner. (Author/MA)

  16. Scientist-Image Stereotypes: The Relationships among Their Indicators

    Science.gov (United States)

    Karaçam, Sedat

    2016-01-01

    The aim of this study is to examine primary school students' scientist-image stereotypes by considering the relationships among indicators. A total of 877 students attending Grades 6 and 7 in Düzce, Turkey participated in this study. The Draw-A-Scientist Test (DAST) was implemented during the 2013-2014 academic year to determine students' images…

  17. Does it really matter that one is a woman scientist?

    Indian Academy of Sciences (India)

    Lawrence

    our roles as mothers or as scientists. Society still stereotypes women in certain roles and does not expect us to break from them easily. To be accepted as a scientist who happens to be a woman is still an uphill task in some areas considered a man's world! A woman is expected to be docile and not ask too many questions.

  18. GIS cartography a guide to effective map design

    CERN Document Server

    Peterson, Gretchen N

    2009-01-01

    Maps, either printed or digital, can create effective communication with bosses, clients, other scientists, and the public. However, entry level GISers often find that map design was given short shrift in their pre-professional life. It is time for the GIS field, which is maturing in other ways, to improve its skills in this area. Based on the author's more than ten years of research and practice in map design, GIS Cartography: A Guide to Effective Map Design provides the tools to create truly sophisticated maps. Packed full of in-depth information and advice, this book covers all facets of ma

  19. Overcoming the obstacles: Life stories of scientists with learning disabilities

    Science.gov (United States)

    Force, Crista Marie

    Scientific discovery is at the heart of solving many of the problems facing contemporary society. Scientists are retiring at rates that exceed the numbers of new scientists. Unfortunately, scientific careers still appear to be outside the reach of most individuals with learning disabilities. The purpose of this research was to better understand the methods by which successful learning disabled scientists have overcome the barriers and challenges associated with their learning disabilities in their preparation and performance as scientists. This narrative inquiry involved the researcher writing the life stories of four scientists. These life stories were generated from extensive interviews in which each of the scientists recounted their life histories. The researcher used narrative analysis to "make sense" of these learning disabled scientists' life stories. The narrative analysis required the researcher to identify and describe emergent themes characterizing each scientist's life. A cross-case analysis was then performed to uncover commonalities and differences in the lives of these four individuals. Results of the cross-case analysis revealed that all four scientists had a passion for science that emerged at an early age, which, with strong drive and determination, drove these individuals to succeed in spite of the many obstacles arising from their learning disabilities. The analysis also revealed that these scientists chose careers based on their strengths; they actively sought mentors to guide them in their preparation as scientists; and they developed coping techniques to overcome difficulties and succeed. The cross-case analysis also revealed differences in the degree to which each scientist accepted his or her learning disability. While some demonstrated inferior feelings about their successes as scientists, still other individuals revealed feelings of having superior abilities in areas such as visualization and working with people. These individuals revealed

  20. Scientist Spotlight Homework Assignments Shift Students' Stereotypes of Scientists and Enhance Science Identity in a Diverse Introductory Science Class.

    Science.gov (United States)

    Schinske, Jeffrey N; Perkins, Heather; Snyder, Amanda; Wyer, Mary

    2016-01-01

    Research into science identity, stereotype threat, and possible selves suggests a lack of diverse representations of scientists could impede traditionally underserved students from persisting and succeeding in science. We evaluated a series of metacognitive homework assignments ("Scientist Spotlights") that featured counterstereotypical examples of scientists in an introductory biology class at a diverse community college. Scientist Spotlights additionally served as tools for content coverage, as scientists were selected to match topics covered each week. We analyzed beginning- and end-of-course essays completed by students during each of five courses with Scientist Spotlights and two courses with equivalent homework assignments that lacked connections to the stories of diverse scientists. Students completing Scientist Spotlights shifted toward counterstereotypical descriptions of scientists and conveyed an enhanced ability to personally relate to scientists following the intervention. Longitudinal data suggested these shifts were maintained 6 months after the completion of the course. Analyses further uncovered correlations between these shifts, interest in science, and course grades. As Scientist Spotlights require very little class time and complement existing curricula, they represent a promising tool for enhancing science identity, shifting stereotypes, and connecting content to issues of equity and diversity in a broad range of STEM classrooms. © 2016 J. N. Schinske et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).