Nature Protocols 3, 1815 (2008). doi:10.1038/nprot.2008.181

Authors: Qinghong Han & Robert M Hoffman

Pyridoxal-5′-phosphate (PLP) is the biologically active form of vitamin B6. Clinical studies suggest that low PLP concentrations are an independent risk factor for cardiovascular and other diseases. However, PLP concentrations are not routinely used for diagnosis because of the lack of a homogeneous,

Nature Protocols 3, 1820 (2008). doi:10.1038/nprot.2008.182

Authors: Sherif S Ebada, Ru Angelie Edrada, Wenhan Lin & Peter Proksch

In the past few decades, marine natural products bioprospecting has yielded a considerable number of drug candidates. Two marine natural products have recently been admitted as new drugs: Prialt (also known as ziconotide) as a potent analgesic for severe chronic pain and Yondelis (known also

Nature Protocols 3, 1832 (2008). doi:10.1038/nprot.2008.184

Authors: Qiang Wang, Adrian A Canutescu & Roland L Dunbrack

SCWRL and MolIDE are software applications for prediction of protein structures. SCWRL is designed specifically for the task of prediction of side-chain conformations given a fixed backbone usually obtained from an experimental structure determined by X-ray crystallography or NMR. SCWRL is a command-line program that

Nature Protocols 3, 1848 (2008). doi:10.1038/nprot.2008.185

Authors: Faqing Huang, Jun He, Yilin Zhang & Yanlin Guo

Biotin-labeled RNA has found broad applications in chemistry, biology and biomedicine. In this protocol, we describe a simple procedure for 5′ RNA biotin labeling by one-step in vitro transcription. A biotin–AMP (adenosine 5′-monophosphate) conjugate, biotin-HDAAMP (adenosine 5′-(6-aminohexyl) phosphoramide; where HDA is 1,6-hexanediamine), is chemically

Nature Protocols 3, 1862 (2008). doi:10.1038/nprot.2008.186

Authors: Linh N Pham, Michelle Kanther, Ivana Semova & John F Rawls

Vertebrates are colonized at birth by complex and dynamic communities of microorganisms that can contribute significantly to host health and disease. The ability to raise animals in the absence of microorganisms has been a powerful tool for elucidating the relationships between animal hosts and their

Nature Protocols 3, 1876 (2008). doi:10.1038/nprot.2008.187

Authors: Stefan C Materna & Paola Oliveri

Regulatory genes form large networks that are fundamental to the developmental program. The protocol presented here describes a general approach to assemble maps of gene regulatory networks (GRNs). It combines high-resolution spatio-temporal profiling of regulatory genes, strategies to perturb gene expression and quantification of perturbation

Nature Protocols 3, 1888 (2008). doi:10.1038/nprot.2008.188

Authors: Myung-Soo Cho, Dong-Youn Hwang & Dong-Wook Kim

Cell-replacement therapy using human embryonic stem cells (hESCs) holds great promise in treating Parkinson's disease. We have recently reported a highly efficient method to generate functional dopaminergic (DA) neurons from hESCs. Our method includes a unique step, the formation of spherical neural masses (SNMs), and

Nature Protocols 3, 1895 (2008). doi:10.1038/nprot.2008.189

Authors: Elisa Michelini, Luca Cevenini, Laura Mezzanotte, Piia Leskinen, Marko Virta, Matti Karp & Aldo Roda

We report a step-by-step protocol describing how to develop and use a yeast-based bioassay for androgen-like compounds. Saccharomyces cerevisiae cells are genetically engineered to express the human androgen receptor (hAR) and the bioluminescent (BL) reporter gene luciferase (from Photinus pyralis) under the control

Nature Protocols 3, 1903 (2008). doi:10.1038/nprot.2008.191

Authors: Tomasz K Wojdacz, Alexander Dobrovic & Lise Lotte Hansen

The base composition of PCR products derived from sodium bisulfite-modified templates is methylation dependent. Hence, methylated and unmethylated, PCR products show different melting profiles when subjected to thermal denaturation. The methylation-sensitive high-resolution melting (MS-HRM) protocol is based on the comparison of the melting profiles of

Nature Protocols 3, 1909 (2008). doi:10.1038/nprot.2008.192

Authors: Jyotsna Chandra, Pranab K Mukherjee & Mahmoud A Ghannoum

Evaluation of fungal biofilm formation can be performed using several techniques. In this protocol, we describe methods used to form Candida biofilms on three different medical device substrates (denture strips, catheter disks and contact lenses) to quantify them and to evaluate their architecture and

Nature Protocols 3, 1925 (2008). doi:10.1038/nprot.2008.193

Authors: Emmanouil Tampakakis, Ikechukwu Okoli & Eleftherios Mylonakis

Traditional antimicrobial screens focus on compounds that block the growth of microbial organisms. A new Caenorhabditis elegans-based bioassay can be used for the identification of antifungal compounds that are effective against Candida albicans. According to the protocol, adult nematodes are infected with C.

Nature Protocols 3, 1932 (2008). doi:10.1038/nprot.2008.194

Authors: Christopher Y Park, Ravindra Majeti & Irving L Weissman

Establishment of robust xenograft models is critical to studying human hematopoiesis in a physiologic setting. Using a recently developed immunodeficient mouse strain, we have established long-term multilineage human grafts and demonstrated their serially transplantability using limited numbers of purified human hematopoietic stem cells (HSCs). Herein,