Nature Methods Application Notes e-UPDATE: 10 April 2012

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10 APRIL 2012  Application Notes bring you the latest information about innovative tools and technologies and their applications in the lab. We hope that you will find this service useful and informative and encourage you to sign up for future Updates to ensure that you never miss one!

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FEATURED APPLICATION NOTE Expresso® CMV system: effortless mammalian expression cloning www.lucigen.com > The Expresso® systems dramatically increase the speed and efficiency of target gene cloning and protein expression. With Expressioneering™, PCR products are cloned instantly and directionally into pre-processed mammalian expression vectors without sample cleanup or enzyme treatment. PDF

		Assessing mitochondrial dysfunction in primary cardiomyocytes www.seahorsebio.com > This Application Note describes a method for profiling mitochondrial function in cells responding to stress. The mitochondrial profile generated in this way provides four parameters of mitochondrial function that can be measured in one experiment: basal respiration rate, ATP-linked respiration, proton leak, and reserve capacity. The results described here suggest that the development of cardiomyocyte injury, in this case caused by an oxidized lipid, increases ATP-linked oxygen consumption, diminishes respiratory efficiency, and depletes the bioenergetic reserve capacity. Seahorse Bioscience recently introduced the XF Cell Mito Stress Test Kit for use with the XF Analyzer, enabling researchers to confidently establish a complete mitochondrial profile with pre-tested and pre-calibrated reagents. PDF

		A rapid, directional RNA-seq library preparation workflow for Illumina® sequencing www.epibio.com > Most current RNA-seq library preparation methods are time-consuming, multistep processes. We describe a workflow that includes the Ribo-Zero™ and ScriptSeq™ v2 Kits that enables researchers to go from total RNA to cluster-ready RNA-seq libraries in less than 1 d. The RNA-seq libraries produced are virtually free of contaminating ribosomal RNA (rRNA) and provide for directional paired-end and multiplex sequencing on Illumina® sequencing platforms. PDF

		Novel Approach in Identification of Substrates for Ligases: Protein Microarrays www.lifesensors.com > Dedicated to providing pioneering reagents as well as proteomic service solutions to all questions ubiquitin related, LifeSensors scientists can turn questions into answers. Perhaps no question is more commonly asked of the ubiquitome than “what are the substrates of my E3?”. A combination of protein microarray expertise and novel ubiquitin research reagents makes LifeSensors uniquely qualified to get you those answers. PDF

		Improving NGS Library Prep with an Open System Liquid Handler www.biooscientific.com > Growing next generation sequencing (NGS) throughput and new, sophisticated multiplexing strategies have significantly increased the number of samples users can prepare. The demand for reproducible and reliable data requires consistency between libraries. To achieve this, the VERSA Mini NGLP, liquid handling workstation has been optimized for NGS library preparation. Using NEXTflex™ library preparation technology in conjunction with the VERSA Mini NGLP, high throughput functionality matched with superior enzyme performance outpaces and improves consistency when compared to manual library preparation. PDF

		Duolink-“In-cell Co-IP” for visualization of protein interactions in situ www.olink.com > Duolink® offers a user-friendly solution for studying protein-protein interactions. Duolink utilizes a pair of antibodies that are capable of quantitatively reporting even weak and transient protein-protein interactions in natively expressing cells either as countable, bright fluorescent spots for a standard fluorescence microscope or via chromogenic detection for brightfield microscopes. It offers all the benefits of traditional coimmunoprecipitation (Co-IP) and western blotting but with better quantitative precision and more information about cell-to-cell variability and target localization. It is also amenable to high throughput in 96 or 384 wells. PDF

		Ribo-Zero Gold Kit: improved RNA-seq results after removal of cytoplasmic and mitochondrial ribosomal RNA www.epibio.com > Ribosomal RNA (rRNA) constitutes the majority (>98%) of total RNA preparations. To avoid wasting sequencing reads, it is necessary to remove this abundant RNA before preparing RNA libraries for deep sequencing. We previously developed Ribo-Zero™ technology for cytoplasmic rRNA removal from intact and degraded RNA. Here, we describe the Ribo-Zero Gold Kit: an improvement to the original Ribo-Zero method that allows removal of mitochondrial as well as cytoplasmic rRNA from total RNA preparations. PDF

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