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  1. No Access

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    Improving Biocontainment with Synthetic Biology: Beyond Physical Containment

    Genetically engineered organisms are per se subject to a biosafety risk assessment to define whether the resulting organism is safe for humans and the environment, either for contained use or environmental rel...

    Markus Schmidt, Lei Pei (2015)

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    A Protocol to Collect Specific Mouse Skeletal Muscles for Metabolomics Studies

    Due to the highly sensitive nature of metabolic states, the quality of metabolomics data depends on the suitability of the experimental procedure. Metabolism could be affected by factors such as the method of ...

    Zhuohui Gan, Zhenxing Fu, Jennifer C. Stowe, Frank L. Powell, Andrew D. McCulloch (2015)

  3. No Access

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    Microarray Approach to Identify the Signaling Network Responsible for Self-Renewal of Human Embryonic Stem Cells

    Here we introduce the representative method to culture HESCs under the feeder and feeder-free conditions, the former of which is used to maintain or expand undifferentiated HESCs, and the latter can be used fo...

    Noboru Sato, Ali Brivanlou (2015)

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    Methods for Derivation of Multipotent Neural Crest Cells Derived from Human Pluripotent Stem Cells

    Multipotent, neural crest cells (NCCs) produce a wide range of cell types during embryonic development. This includes melanocytes, peripheral neurons, smooth muscle cells, osteocytes, chondrocytes, and adipocy...

    John Avery, Stephen Dalton (2015)

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    Biodegradation Prediction Tools

    Experimental approaches for determining the environmental fate of new molecules generated by the modern chemical and pharmaceutical industry cannot cope with the pace at which new of these substances are synth...

    Florencio Pazos, Víctor de Lorenzo (2015)

  6. No Access

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    Protocols for Measurement of Naphthenic Acids in Aqueous Samples

    Naphthenic acids (NAs), a group of polar organic carboxylic acids that naturally occur in crude oil, have been of concern since the turn of the twentieth century due to corrosion of petroleum refineries. In th...

    Lisa Brown, Ania Ulrich (2015)

  7. No Access

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    Using Semantic Similarities and csbl.go for Analyzing Microarray Data

    Cellular phenotypes result from the combined effect of multiple genes, and high-throughput techniques such as DNA microarrays and deep sequencing allow monitoring this genomic complexity. The large scale of th...

    Kristian Ovaska (2015)

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    Normalization of Affymetrix miRNA Microarrays for the Analysis of Cancer Samples

    microRNA (miRNA) microarray normalization is a critical step for the identification of truly differentially expressed miRNAs. This is particularly important when dealing with cancer samples that have a global ...

    Di Wu, Michael P. Gantier (2015)

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    Analysis of microRNA Microarrays in Cardiogenesis

    microRNAs are a subclass of noncoding RNAs which have been demonstrated to play pivotal roles in multiple cellular mechanisms. microRNAs are small RNA molecules of 22–24 nt in length capable of modulating prot...

    Diego Franco, Fernando Bonet, Francisco Hernandez-Torres, Estefania Lozano-Velasco (2015)

  10. No Access

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    Ontology-Based Analysis of Microarray Data

    The importance of semantic-based methods and algorithms for the analysis and management of biological data is growing for two main reasons. From a biological side, knowledge contained in ontologies is more and...

    Agapito Giuseppe, Marianna Milano (2015)

  11. No Access

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    Directed Myogenic Differentiation of Human Induced Pluripotent Stem Cells

    Patient-derived induced pluripotent stem cells (iPSCs) have opened the door to recreating pathological conditions in vitro using differentiation into diseased cells corresponding to each target tissue. Yet for...

    Emi Shoji, Knut Woltjen, Hidetoshi Sakurai (2015)

  12. No Access

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    Functional Analysis of microRNA in Multiple Myeloma

    MicroRNAs (miRNAs) are short non coding RNAs that regulate the gene expression and play a relevant role in physiopathological mechanisms such as development, proliferation, death, and differentiation of normal...

    Maria Teresa Di Martino Ph.D., Nicola Amodio, Pierfrancesco Tassone M.D. (2015)

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    Protocols for Probing Genome Architecture of Regulatory Networks in Hydrocarbon and Lipid Microorganisms

    Genome architecture and the regulation of gene expression are expected to be interdependent. Understanding this interdependence is key to successful genome engineering. Evidence for nonrandom arrangement of ge...

    Costas Bouyioukos, Mohamed Elati, François Képès (2015)

  14. No Access

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    Method for Preparation and Electroporation of S. aureus and S. epidermidis

    For bacterial species that are not known to be naturally competent, such as Staphylococcus aureus and Staphylococcus epidermidis, electroporation is an efficient method for introducing genetic material into the c...

    Melinda R. Grosser, Anthony R. Richardson (2015)

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    Characterization of Bacterial Symbionts in Deep-Sea Fauna: Protocols for Sample Conditioning, Fluorescence In Situ Hybridization, and Image Analysis

    Symbioses with bacteria are key adaptations allowing various groups of metazoans to reach high biomasses at deep sea reducing habitats including hydrothermal vents and cold seeps. Characterizing these associat...

    Sébastien Duperron (2015)

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    DNA- and RNA-Based Stable Isotope Probing of Hydrocarbon Degraders

    The microbial degradation of hydrocarbons in contaminated environments can be driven by distinct aerobic and anaerobic populations. While the physiology and biochemistry of selected degraders isolated in pure ...

    Tillmann Lueders (2015)

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    Dopaminergic Differentiation of Human Embryonic Stem Cells on PA6-Derived Adipocytes

    Human embryonic stem cells (hESCs) are a promising source for cell replacement therapies. Parkinson’s disease is one of the candidate diseases for the cell replacement therapy since the motor manifestations of...

    M. Oktar Guloglu, Anna Larsen (2015)

  18. No Access

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    GC-MS-Based Determination of Mass Isotopomer Distributions for 13C-Based Metabolic Flux Analysis

    13C-based metabolic flux analysis is currently the most powerful tool to determine intracellular reaction rates in biological systems and valuable, e.g., for the identification of metabolic enginee...

    Andreas Schmitz, Birgitta E. Ebert, Lars M. Blank (2015)

  19. No Access

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    Protocol for Evaluating the Biological Stability of Fuel Formulations and Their Relationship to Carbon Steel Biocorrosion

    The microbial metabolism of conventional and alternative fuels can be associated with the biocorrosion of the mostly carbon steel energy infrastructure. This phenomenon is particularly acute in anaerobic sulfa...

    Renxing Liang, Joseph M. Suflita (2015)

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    Generating Enriched Metagenomes from Active Microorganisms with DNA Stable Isotope Probing

    Cultivation-dependent methods have long been used to characterise the physiology of microorganisms after they have been isolated from the environment. In contrast, cultivation-independent methods help better i...

    Carolina Grob, Martin Taubert, Alexandra M. Howat, Oliver J. Burns, Yin Chen (2015)

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