Tuesday, July 11, 2017

Nature Methods Application Notes e-UPDATE: 11 July 2017

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11 July 2017 
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Label-free, real-time live-cell assays for spheroids: IncuCyte® bright-field analysis
www.essenbioscience.com/en/ >
A growing body of evidence suggests that more relevant and translational observations can be made with micro-tissues and organoids compared to 2D monolayer cell models. This is most notable in the cancer biology and hepatotoxicity field. For example, tumor spheroids exhibit more relevant morphology and increased cell survival compared to 2D cultures and have a hypoxic core. Current methods for assessing the growth and shrinkage of tumor spheroids are limited by one or more of the following: (1) assay workflows that are time-consuming, expensive or laborious, (2) a requirement to label the cells (e.g. a fluorescent probe) which may perturb the biology and may not be amenable to primary tissue, (3) single time-point readouts that do not report the full timecourse, (4) indirect readouts (e.g. ATP) that may overlook valuable morphological insight and/or mis-report cell growth.

In this application note we describe methods and validation data for miniaturized (96/384-well) live-cell tumor spheroid assays that are based on non-invasive bright-field image analysis performed with the IncuCyte® S3 Spheroid software module. Tumor spheroids are formed in ultra-low attachment (ULA) plates and monitored for size and morphology for up to 2 weeks. These assays are flexible, simple to run and provide automated and direct measures of tumor size in real-time.


A humanized phenotypic screening platform for chronic pain
www.censobio.com >
www.Cellectricon.com >
Censo Biotechnologies and Cellectricon have joined forces to develop a first-in-kind humanized drug discovery platform to target chronic pain. The platform is based on human induced pluripotent stem cell–derived neurons in combination with Cellectricon's Cellaxess® Elektra screening system. The combination of highly functional screening with a human cell type of relevance for chronic pain has the potential to enable the generation of better drug candidates for this condition and other diseases.

Gibson Assembly® Primer-Bridge End Joining (PBnJ™) Cloning
www.syntheticgenomics.com >
Gibson Assembly® cloning has proven to be useful as a molecular biology technique for the seamless assembly of synthetic and natural genes and large-scale genetic pathways. Notably, Gibson Assembly cloning has enabled the synthesis of the first bacterial genome1, the first synthetic cell2, and the first minimal cell3. Additionally, the Gibson Assembly method has been utilized for genetic recoding (genome-wide codon removal)4, the engineering of Cre recombinase for improved site-specificity5, and has been incorporated into a one-step method for cloning gRNA for the CRISPR-Cas9 system6.

Turning neuroscience data into insight in the 21st century
www.metacell.us >
The modern research and industrial approach to neuroscience involves an increasingly vast assortment of data collection methods and data handling approaches. While data collection and accumulation are expanding, approaches to data management and insight gathering are still lacking.

Match & Scratch Barcodes: Tools for the Demultiplexing and Extraction of Target Sequences from PacBio Amplicon Data
www.jax.org >
One of the major challenges for the downstream analysis of amplicon data is to first demultiplex Fastq files based on the ligation of different oligonucleotides combinations. Match & Scratch Barcodes are a set of bioinformatics tools that support the analysis of PacBio sequenced long read amplicon data by detecting forward and reverse end adapter sequences, generic adapters attachedto the region specific oligos, multiple number of region specific oligos of variable length for the extraction of sequences of interest.

INCELLIS: Perfect tool to qualify the cell labelling before using a high end microscope
www.bertin-instruments.com >
Centrosome is an organelle implicated in cell cycle regulation. During cell division, the two centrosomes serve as anchors to guide the chromosomes and divide them into two equitable batches to form the two daughter cells. An aberrant number of centrosomes in a cell is often associated with cancer. Expression of GFP-centrin recombinant protein into in vitro cell culture allows direct visualization of centriole behavior in living cells in different experimental conditions. Nevertheless, as it is a small organelle, imaging of GFP-centrin protein into centrosome requires high sensitivity in fluorescence.

Robotic Microscopy with the Nikon Ti2 for high-content analysis applications
www.nikon.com >
Robotic Microscopy—a combination of high-content screening methods—enables multivariate experimental approaches with large cell populations and member-level sensitivity. Here we explore how the new Nikon Ti2 line of inverted research microscopes is uniquely suited to Robotic Microscopy applications, focusing on work utilizing induced pluripotent stem cells (iPSCs) as disease models in drug screening.


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