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Nature Protocols
Efficient imaging of amyloid deposits in Drosophila models of human amyloidoses
Wed, 04/28/2010 - 23:00Efficient imaging of amyloid deposits in Drosophila models of human amyloidoses
Nature Protocols 5, 935 (2010). doi:10.1038/nprot.2010.41
Authors: Ina Berg, K Peter R Nilsson, Stefan Thor & Per Hammarström
Drosophila melanogaster is emerging as an important model system for neurodegenerative disease research. In this protocol, we describe an efficient method for imaging amyloid deposits in the Drosophila brain, by the use of a luminescent-conjugated oligothiophene (LCO), p-FTAA polymer probe. We also demonstrate
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Synthesis of alkyl- and aryl-amino-substituted anthraquinone derivatives by microwave-assisted copper(0)-catalyzed Ullmann coupling reactions
Wed, 04/28/2010 - 23:00Synthesis of alkyl- and aryl-amino-substituted anthraquinone derivatives by microwave-assisted copper(0)-catalyzed Ullmann coupling reactions
Nature Protocols 5, 945 (2010). doi:10.1038/nprot.2010.63
Authors: Younis Baqi & Christa E Müller
This protocol describes the efficient, generally applicable Ullmann coupling reaction of bromaminic acid with alkyl- or aryl-amines in phosphate buffer under microwave irradiation using elemental copper as a catalyst. The reaction leads to a number of biologically active compounds. As a prototypical example, the synthesis
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The learned safety paradigm as a mouse model for neuropsychiatric research
Wed, 04/28/2010 - 23:00The learned safety paradigm as a mouse model for neuropsychiatric research
Nature Protocols 5, 954 (2010). doi:10.1038/nprot.2010.64
Authors: Daniela D Pollak, Francisco J Monje & Gert Lubec
Fear conditioning is one of the most widely used animal models for studying the neurobiological basis of fear and anxiety states. Conditioned inhibition of fear (or learned safety), however, is a relatively unexplored behavioral paradigm addressing the aspect of regulation of fear, which is central
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Production of mice using iPS cells and tetraploid complementation
Wed, 04/28/2010 - 23:00Production of mice using iPS cells and tetraploid complementation
Nature Protocols 5, 963 (2010). doi:10.1038/nprot.2010.61
Authors: Xiao-Yang Zhao, Zhuo Lv, Wei Li, Fanyi Zeng & Qi Zhou
Induced pluripotent stem cells (iPSCs) are considered to be an attractive alternative to embryonic stem cells (ESCs) and may provide great potential for clinical applications in regenerative medicine. Although possessing characteristics similar to ESCs, the true pluripotency of these newly studied iPSCs was not known
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Assaying proliferation and differentiation capacity of stem cells using disaggregated adult mouse epidermis
Wed, 04/21/2010 - 23:00Assaying proliferation and differentiation capacity of stem cells using disaggregated adult mouse epidermis
Nature Protocols 5, 898 (2010). doi:10.1038/nprot.2010.39
Authors: Kim B Jensen, Ryan R Driskell & Fiona M Watt
In this protocol, we describe how to isolate keratinocytes from adult mouse epidermis, fractionate them into different sub-populations on the basis of cell surface markers and examine their function in an in vivo skin reconstitution assay with disaggregated neonatal dermal cells. We also describe
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Adipose angiogenesis: quantitative methods to study microvessel growth, regression and remodeling in vivo
Wed, 04/21/2010 - 23:00Adipose angiogenesis: quantitative methods to study microvessel growth, regression and remodeling in vivo
Nature Protocols 5, 912 (2010). doi:10.1038/nprot.2010.46
Authors: Yuan Xue, Sharon Lim, Ebba Bråkenhielm & Yihai Cao
Genetic and diet-induced rodent obesity models provide outstanding opportunities to study the role of angiogenesis and vascular remodeling in modulation of adipogenesis and obesity. In this study, we describe methods to quantitatively study adipose angiogenesis and vascular remodeling on the basis of immunohistochemical analyses. Fresh
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Conversion of adult mouse unipotent germline stem cells into pluripotent stem cells
Wed, 04/21/2010 - 23:00Conversion of adult mouse unipotent germline stem cells into pluripotent stem cells
Nature Protocols 5, 921 (2010). doi:10.1038/nprot.2010.44
Authors: Kinarm Ko, Marcos J Araúzo-Bravo, Julee Kim, Martin Stehling & Hans R Schöler
Germline stem cells (GSCs), often called spermatogonial stem cells, are unipotent stem cells that can give rise only to gametes. Under defined culture conditions, unipotent GSCs can be converted into pluripotent stem cells, termed as germline-derived pluripotent stem (gPS) cells. gPS cells can be differentiated
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Detection of Mycoplasma in cell cultures
Wed, 04/21/2010 - 23:00Detection of Mycoplasma in cell cultures
Nature Protocols 5, 929 (2010). doi:10.1038/nprot.2010.43
Authors: Lesley Young, Julia Sung, Glyn Stacey & John R Masters
Mycoplasma is a prokaryotic organism that is a frequent and occult contaminant of cell cultures. This organism can modify many aspects of cell physiology, rendering experiments that are conducted with contaminated cells worthless. Because of their small size, Mycoplasmas can pass through filters used to
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The use of mesenchymal stem cells in collagen-based scaffolds for tissue-engineered repair of tendons
Wed, 04/14/2010 - 23:00The use of mesenchymal stem cells in collagen-based scaffolds for tissue-engineered repair of tendons
Nature Protocols 5, 849 (2010). doi:10.1038/nprot.2010.14
Authors: David L Butler, Cynthia Gooch, Kirsten R C Kinneberg, Gregory P Boivin, Marc T Galloway, V Sanjit Nirmalanandhan, Jason T Shearn, Nathaniel A Dyment & Natalia Juncosa-Melvin
Tendon and ligament injuries are significant contributors to musculoskeletal injuries. Unfortunately, traditional methods of repair are not uniformly successful and can require revision surgery. Our research is focused on identifying appropriate animal injury models and using tissue-engineered constructs (TECs) from bone-marrow-derived mesenchymal stem cells and
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Investigation of bacterial chemotaxis in flow-based microfluidic devices
Wed, 04/14/2010 - 23:00Investigation of bacterial chemotaxis in flow-based microfluidic devices
Nature Protocols 5, 864 (2010). doi:10.1038/nprot.2010.18
Authors: Derek L Englert, Michael D Manson & Arul Jayaraman
The plug-in-pond and capillary assays are convenient methods for measuring attractant and repellent bacterial chemotaxis. However, these assays do not provide quantitative information on the extent of migration and are not well-suited for investigating repellent taxis. Here, we describe a protocol for a flow-based microfluidic
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High-stringency tandem affinity purification of proteins conjugated to ubiquitin-like moieties
Wed, 04/14/2010 - 23:00High-stringency tandem affinity purification of proteins conjugated to ubiquitin-like moieties
Nature Protocols 5, 873 (2010). doi:10.1038/nprot.2010.40
Authors: Filip Golebiowski, Michael H Tatham, Akihiro Nakamura & Ronald T Hay
The post-translational modification of proteins with ubiquitin and ubiquitin-like proteins (Ubl) is vital to many cellular functions, and thus the identification of Ubl targets is key to understanding their function. In most cases, only a small proportion of the cellular pool of proteins is found
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The HADDOCK web server for data-driven biomolecular docking
Wed, 04/14/2010 - 23:00The HADDOCK web server for data-driven biomolecular docking
Nature Protocols 5, 883 (2010). doi:10.1038/nprot.2010.32
Authors: Sjoerd J de Vries, Marc van Dijk & Alexandre M J J Bonvin
Computational docking is the prediction or modeling of the three-dimensional structure of a biomolecular complex, starting from the structures of the individual molecules in their free, unbound form. HADDOCK is a popular docking program that takes a data-driven approach to docking, with support for a
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Generating heparan sulfate saccharide libraries for glycomics applications
Wed, 04/07/2010 - 23:00Generating heparan sulfate saccharide libraries for glycomics applications
Nature Protocols 5, 821 (2010). doi:10.1038/nprot.2010.17
Authors: Andrew K Powell, Yassir A Ahmed, Edwin A Yates & Jeremy E Turnbull
Natural and semi-synthetic heparan sulfate (HS) saccharide libraries are a valuable resource for investigating HS structure–function relationships, enabling high-throughput glycomics studies. Owing to the difficulty of chemical or in vitro enzymatic synthesis of HS saccharides, the structural diversity displayed in saccharides from tissue or
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Analysis of protein S-acylation by gas chromatography–coupled mass spectrometry using purified proteins
Wed, 04/07/2010 - 23:00Analysis of protein S-acylation by gas chromatography–coupled mass spectrometry using purified proteins
Nature Protocols 5, 834 (2010). doi:10.1038/nprot.2010.33
Authors: Nadav Sorek & Shaul Yalovsky
S-acylation, also known as palmitoylation, involves the attachment of acyl fatty acids to thiol groups of cysteine residues through a reversible thioester bond. Owing to its reversibility, S-acylation is important in regulation of diverse signaling cascades, including Ras-associated cancers in mammals, stress response
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In vivo single-cell excitability probing of neuronal ensembles in the intact and awake developing Xenopus brain
Wed, 04/07/2010 - 23:00In vivo single-cell excitability probing of neuronal ensembles in the intact and awake developing Xenopus brain
Nature Protocols 5, 841 (2010). doi:10.1038/nprot.2010.10
Authors: Derek Dunfield & Kurt Haas
Sensory experience can elicit long-lasting plasticity of both single neurons and ensemble neural circuit response properties during embryonic development. To investigate their relationship, one must image functional responses of large neuronal populations simultaneously with single-cell resolution. In this protocol, we describe a noninvasive approach to
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