Revolutionizing scientific communication and collaboration

This presentation introduces new web-based ways of scientific communication and collaboration. It focuses on wikis and the _First Online EMBL PhD Symposium_ as an example of an online conference

A quick trip through openness, freedom and transparency

This talk aims to give scientists an introduction to the concepts of openness, freedom and transparency and their applications (not only) for science. It covers the topics of open source, open formats, Creative Commons, open access, and open science/knowledge. A video of the talk is available on the author's website.
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The What, Why and How of openness in science

We give a short introduction to open science followed by an overview of Creative Commons and open source licenses

Gene autoregulation by 3' UTR-derived bacterial small RNAs

Negative feedback regulation, that is the ability of a gene to repress its own synthesis, is the most abundant regulatory motif known to biology. Frequently reported for transcriptional regulators, negative feedback control relies on binding of a transcription factor to its own promoter. Here, we report a novel mechanism for gene autoregulation in bacteria relying on small regulatory RNA (sRNA) and the major endoribonuclease, RNase E. TIER-seq analysis (transiently-inactivating-an-endoribonuclease-followed-by-RNA-seq) revealed similar to 25,000 RNase E-dependent cleavage sites in Vibrio cholerae, several of which resulted in the accumulation of stable sRNAs. Focusing on two examples, OppZ and CarZ, we discovered that these sRNAs are processed from the 3' untranslated region (3' UTR) of the oppABCDF and carAB operons, respectively, and basepair with their own transcripts to inhibit translation. For OppZ, this process also triggers Rho-dependent transcription termination. Our data show that sRNAs from 3' UTRs serve as autoregulatory elements allowing negative feedback control at the post-transcriptional level

A computational screen for type I polyketide synthases in metagenomics shotgun data

BACKGROUND: Polyketides are a diverse group of biotechnologically important secondary metabolites that are produced by multi domain enzymes called polyketide synthases (PKS). METHODOLOGY/PRINCIPAL FINDINGS: We have estimated frequencies of type I PKS (PKS I) – a PKS subgroup – in natural environments by using Hidden-Markov-Models of eight domains to screen predicted proteins from six metagenomic shotgun data sets. As the complex PKS I have similarities to other multi-domain enzymes (like those for the fatty acid biosynthesis) we increased the reliability and resolution of the dataset by maximum-likelihood trees. The combined information of these trees was then used to discriminate true PKS I domains from evolutionary related but functionally different ones. We were able to identify numerous novel PKS I proteins, the highest density of which was found in Minnesota farm soil with 136 proteins out of 183,536 predicted genes. We also applied the protocol to UniRef database to improve the annotation of proteins with so far unknown function and identified some new instances of horizontal gene transfer. CONCLUSIONS/SIGNIFICANCE: The screening approach proved powerful in identifying PKS I sequences in large sequence data sets and is applicable to many other protein families

A Mission to Explore the Pioneer Anomaly

The Pioneer 10 and 11 spacecraft yielded the most precise navigation in deep space to date. These spacecraft had exceptional acceleration sensitivity. However, analysis of their radio-metric tracking data has consistently indicated that at heliocentric distances of $\sim 20-70$ astronomical units, the orbit determinations indicated the presence of a small, anomalous, Doppler frequency drift. The drift is a blue-shift, uniformly changing with a rate of $\sim(5.99 \pm 0.01)\times 10^{-9}$ Hz/s, which can be interpreted as a constant sunward acceleration of each particular spacecraft of $a_P = (8.74 \pm 1.33)\times 10^{-10} {\rm m/s^2}$. This signal has become known as the Pioneer anomaly. The inability to explain the anomalous behavior of the Pioneers with conventional physics has contributed to growing discussion about its origin. There is now an increasing number of proposals that attempt to explain the anomaly outside conventional physics. This progress emphasizes the need for a new experiment to explore the detected signal. Furthermore, the recent extensive efforts led to the conclusion that only a dedicated experiment could ultimately determine the nature of the found signal. We discuss the Pioneer anomaly and present the next steps towards an understanding of its origin. We specifically focus on the development of a mission to explore the Pioneer Anomaly in a dedicated experiment conducted in deep space.Comment: 8 pages, 9 figures; invited talk given at the 2005 ESLAB Symposium "Trends in Space Science and Cosmic Vision 2020", 19-21 April 2005, ESTEC, Noordwijk, The Netherland

Fundamental Physics with the Laser Astrometric Test Of Relativity

The Laser Astrometric Test Of Relativity (LATOR) is a joint European-U.S. Michelson-Morley-type experiment designed to test the pure tensor metric nature of gravitation - a fundamental postulate of Einstein's theory of general relativity. By using a combination of independent time-series of highly accurate gravitational deflection of light in the immediate proximity to the Sun, along with measurements of the Shapiro time delay on interplanetary scales (to a precision respectively better than 0.1 picoradians and 1 cm), LATOR will significantly improve our knowledge of relativistic gravity. The primary mission objective is to i) measure the key post-Newtonian Eddington parameter \gamma with accuracy of a part in 10^9. (1-\gamma) is a direct measure for presence of a new interaction in gravitational theory, and, in its search, LATOR goes a factor 30,000 beyond the present best result, Cassini's 2003 test. The mission will also provide: ii) first measurement of gravity's non-linear effects on light to ~0.01% accuracy; including both the Eddington \beta parameter and also the spatial metric's 2nd order potential contribution (never measured before); iii) direct measurement of the solar quadrupole moment J2 (currently unavailable) to accuracy of a part in 200 of its expected size; iv) direct measurement of the "frame-dragging" effect on light by the Sun's gravitomagnetic field, to 1% accuracy. LATOR's primary measurement pushes to unprecedented accuracy the search for cosmologically relevant scalar-tensor theories of gravity by looking for a remnant scalar field in today's solar system. We discuss the mission design of this proposed experiment.Comment: 8 pages, 9 figures; invited talk given at the 2005 ESLAB Symposium "Trends in Space Science and Cosmic Vision 2020," 19-21 April 2005, ESTEC, Noodrwijk, The Netherland

Sustainable Innovation in a Multi-University Master Course

Mobility, multi-locality, and transnational migration are current social developments among the population of the European Union. These social developments in society and companies, linked to the challenges of sustainability, lead to new requirements for working in the European Union. Teaching and learning in higher education needs to adapt to these requirements. As a result, new and innovative teaching and learning practices in higher education should provide competencies for transnational teamwork in the curriculum of tomorrow's engineers in order to ensure their competitiveness in the job market and advantage in their future careers. Thirteen European students from four countries participated in a new project-based course, called the "European Engineering Team". Students focused on the development of two innovative and sustainable products. The goal of this paper is to present the thermal pallet cover, which is the result of the first one-year transnational and sustainability-oriented project. This paper also aims to present the process of performing the project. It provides the overview and discussion of engineering and management tasks that students completed in the transnational environment, working remotely at their own campuses between scheduled transnational meetings. The work contributes to project-oriented learning that may constitute a basis for teaching holistic engineering courses at mechanical and industrial engineering departments

A Nitrile Hydratase in the Eukaryote Monosiga brevicollis

Bacterial nitrile hydratase (NHases) are important industrial catalysts and waste water remediation tools. In a global computational screening of conventional and metagenomic sequence data for NHases, we detected the two usually separated NHase subunits fused in one protein of the choanoflagellate Monosiga brevicollis, a recently sequenced unicellular model organism from the closest sister group of Metazoa. This is the first time that an NHase is found in eukaryotes and the first time it is observed as a fusion protein. The presence of an intron, subunit fusion and expressed sequence tags covering parts of the gene exclude contamination and suggest a functional gene. Phylogenetic analyses and genomic context imply a probable ancient horizontal gene transfer (HGT) from proteobacteria. The newly discovered NHase might open biotechnological routes due to its unconventional structure, its new type of host and its apparent integration into eukaryotic protein networks

Relative amino acid composition signatures of organisms and environments

BACKGROUND: Identifying organism-environment interactions at the molecular level is crucial to understanding how organisms adapt to and change the chemical and molecular landscape of their habitats. In this work we investigated whether relative amino acid compositions could be used as a molecular signature of an environment and whether such a signature could also be observed at the level of the cellular amino acid composition of the microorganisms that inhabit that environment. METHODOLOGIES/PRINCIPAL FINDINGS: To address these questions we collected and analyzed environmental amino acid determinations from the literature, and estimated from complete genomic sequences the global relative amino acid abundances of organisms that are cognate to the different types of environment. Environmental relative amino acid abundances clustered into broad groups (ocean waters, host-associated environments, grass land environments, sandy soils and sediments, and forest soils), indicating the presence of amino acid signatures specific for each environment. These signatures correlate to those found in organisms. Nevertheless, relative amino acid abundance of organisms was more influenced by GC content than habitat or phylogeny. CONCLUSIONS: Our results suggest that relative amino acid composition can be used as a signature of an environment. In addition, we observed that the relative amino acid composition of organisms is not highly determined by environment, reinforcing previous studies that find GC content to be the major factor correlating to amino acid composition in living organisms.AM was supported by Fundação para a Ciência e a Tecnologia, Portugal, through the postdoctoral grant SFRH/BPD/72256/2010. RA was partially supported by the Ministerio de Ciencia e Innovación (Spain) through grant BFU2010-17704, and by the Generalitat de Catalunya through a grant for research group 2009SGR809. MAS was supported in part by a grant from the US Public Health Service (RO1-GM30054). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Authors wish to thank Albert Sorribas, Enrique Herrero and Ester Vilaprinyo for critical reading of the manuscript and Ester Vilaprinyo for assistance with Wolfram Mathematica software.publishe