Tuesday, May 9, 2017

Nature Methods Application Notes e-UPDATE: 9 May 2017

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9 May 2017 
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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.

Real-time visualization of DNA structural transitions under mechanical stress using high-resolution optical tweezers and multi-color fluorescence microscopy
lumicks.com >
Single-molecule force spectroscopy (SMFS) tools are widely used to study structural transitions of DNA during overstretching. However, as many of these tools only provide global information, the exact mechanisms that occur during these transitions remain unclear. Combining SMFS with visualization of local information could resolve this problem. In this application note we will discuss how LUMICKS' C-Trap™ technology combines high-resolution optical tweezers as a SMFS tool with confocal fluorescence microscopy to monitor the transition of double-stranded (ds) DNA to single-stranded (ss) DNA upon applying mechanical stress.

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.

APD SpectBT: Arduino-based mobile vis-Spectrophotometer
www.a-star.edu.sg >
Quantification of samples is an integral step in numerous biological and chemical experiments. Spectrophotometers are often used together with colorimetric assays that react with the compound of interest in the samples. However, spectrophotometers are often costly, bulky and immobile. To increase the convenience and ease the process of spectrophotometry, the APD SpectBT was developed using the Arduino-based platform to create a smartphone dependent mobile spectrophotometer. Through a Bluetooth® connection, users can use a micro-USB portable spectrophotometer and send the readings to the smartphone app to get visible light absorbance readings conveniently. With the portable SpectBT device and app, users can easily perform spectrophotometry on the go in the field and immediate environments conveniently and rapidly.


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