Nature Methods Application Notes e-UPDATE: 9 August 2016

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9 August 2016  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 HyVolution—the smart path to confocal super-resolution www.leica-microsystems.com/ > Super-resolution refers to any device or method that can resolve better than the classical Abbe limit. Apart from infinite super-resolution techniques such as STED (stimulated emission depletion) and SMLM (single-molecule localization methods) that can theoretically resolve to any detail, there are also methods for limited super-resolution. Here we present HyVolution by Leica, which merges optical super-resolution and computational super-resolution. The optical part is provided by confocal microscopy, and the computational part by deconvolution. Lateral resolution of 140 nm is demonstrated. HyVolution offers multiple fluorescence recording in truly simultaneous mode. PDF

		MAV-seq: Management, Analysis and Visualization of Sequence Data www.jax.org > The increasing amount of heterogeneous Next Generation Sequencing (NGS) data generated today necessitates a robust platform for the efficient data storage, management, pre-processing, quality checking, analysis and visualization. Addressing each of these categories is a tremendous undertaking requiring high-level expertise from various disciplines. The typical genomic research laboratories do not always posses these resources, thus, we have developed a scientific solution to assist researchers dealing with the practical issues associated to the high throughput genomic data. We present MAV-seq as a robust platform, which facilitates the management of samples metadata and NGS data pre-processing, quality assessment and visualization. MAV-seq provides interactive modular data flow, which transparently integrates interoperability, structure, standardization, security, controlled accessibility, management of genomic studies and their sample metadata associated with datasets of enormous size and diversity. PDF

		A Novel Set of Serum-Free, Xeno-Free Differentiation Media for Adipogenesis, Osteogenesis and Chondrogenesis of Human Mesenchymal Stem Cells from Various Tissue Sources www.bioind.com/ > Human mesenchymal stem cells (hMSCs) are multipotent adult stem cells that can be isolated from various tissues as well as generated in vitro from hESCs and iPS cells. hMSCs have at least trilineage differentiation potential in vitro (into fat, bone, and cartilage cells), and it is part of the Minimal Experimental Criteria for MSC proposed by the International Society for Cellular Therapy (ISCT). In addition, differentiation of hMSCs into specific lineage provides the basis for the use of human MSC in cell therapy applications. Either undifferentiated or differentiated, hMSCs can be used for in vivo implantation into damaged tissue sites. The differentiation potential may differ in relation to the culture condition and the source of hMSCs, and it is still unknown which source should be used for each specific disease. PDF

		APD Colony Counter App: Using Watershed Algorithm for improved colony counting www.a-star.edu.sg > The counting of colonies to quantitate bacteria is an important process in labs for research, clinical diagnosis, and environmental monitoring e.g. in water. Generally counted manually, progress in technology has automated the process through colony counters that can be purchased but can be costly. While efficient, there remains also a challenge correctly detecting clustered colonies compromising inaccurate counts. Leveraging on the smartphone camera, we developed an app that processes images of colony plates and automatically counts them. To provide more accurate counts, the watershed algorithm with distance transform was incorporated into the segmentation and found to distinguish clustered or partially merged colonies better. This app, the APD Colony Counter app, thus transforms the smartphone into a portable colony counter, making the once laborious and tedious process manual colony counting, more accurate, automated and on-the-go. PDF

		Advances in Flavivirus research applications: new techniques using the FastPrep-24 5G sample prep system www.mpbio.com/ > The FastPrep-24 5G is the most innovative bead-beating sample-preparation instrument and produces quantitative, thorough and rapid grinding, lysis and homogenization of routine and resistant samples. PDF

		Performing efficient sample preparation with hard tumor tissue: Precellys® bead-beating homogenizer solution www.bertin-technologies.com/ > The Precellys® Evolution is the most efficient homogenizer based on bead-beating technology. It combines high flexibility and high efficiency for either routine or R&D projects. The instrument's unique figure-eight multidirectional motion provides the same high level of energy and homogenization efficiency to all the tubes. PDF

		Variation of homogenization time to optimize yield and quality of DNA extraction from S. cerevisiae suspension www.bio.analytik-jena.com > Analytik Jena's SpeedMill PLUS in combination with innuSPEED Bacteria/Fungi DNA Kit provides a complete system for homogenization of starting material and extraction of DNA. PDF

 

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