Volume 13 Issue 8, August 2016

To the tune of a classical guitar, finding a way to watch learning as it happens.

It is important to understand both what a classification metric expresses and what it hides.

Genome editing marks cells in developing fish for lineaging studies.

Nanobodies that are stable only in the presence of their antigen can be harnessed to manipulate or detect antigen-expressing cells.

A fluorescent NAD⁺ biosensor targeted to specific cellular compartments detects local fluctuation in NAD⁺ concentration.

Fragmenting transcripts after 4-thiouridine incorporation allows the quantification of even short-lived noncoding RNA.

A luciferin analog enables highly sensitive bioluminescent imaging from deep within biological tissue samples.

Labs can generate neurons from pluripotent stem cells to study basic biology and to model disease. Protocols are getting more robust, and labs add personal preferences.

Crowded transcript signals are resolved by cross-correlation or by gel expansion microscopy.

A sequencing approach, m⁶A-LAIC-seq, globally quantifies the proportion of m⁶A-modified transcripts of a specific gene and the differential m⁶A modification levels among its isoforms.

Photoacoustic imaging (PAI) can bridge the gap between high resolution optical imaging and deep tissue imaging applications. This Review introduces PAI as well as various implementations for a range of biological applications.

This Review covers genetically encoded and exogenous contrast agents for photoacoustic imaging and offers guidance for choosing optimal probes for biological applications on the basis of photophysical properties, targeting and performance.

A newly developed algorithm enabled clustering of all 256 million (66 million identified and 190 million unidentified) peptide MS/MS spectra available in the PRIDE Archive database, allowing the detection of millions of consistently unidentified spectra across different data sets, of which roughly 20% could be identified using multiple complementary analysis tools.

Correlation fluorescent in situ hybridization (corrFISH) makes it possible to quantify abundant transcripts using sequential barcoded hybridization, despite high spot density in images.

PALM and STORM are powerful methods for studying membrane-protein clustering. However, fluorophore blinking can lead to miscounting artifacts. A new method shows that varying label density works for artifact-free analysis of membrane-protein nanoclusters.

Reversible cryo-arrest allows consecutive super-resolution and functional imaging of molecular patterns in the same mammalian cell. This method was used to study the evolution of receptor tyrosine kinase reaction patterns at multiple scales.

When studying neural circuitry, the ablation of synapses may be an alternative to optogenetic manipulation of neurons. A genetically encoded tool called GFE3 eliminates inhibitory inputs into neurons expressing GFE3.

ExFISH extends expansion microscopy to single-molecule RNA imaging, enabling super-resolution imaging of diverse RNAs in cells and tissues on conventional microscopes. The method enables multiplexed imaging of RNA and improved RNA quantitation.

UMI-4C is a rapid, simplified barcoding approach to targeted chromatin conformation capture that produces high-complexity libraries from low sample input, is easily multiplexed and gives a quantitative, statistically defined readout.

m⁶A-LAIC-seq quantifies the levels of N⁶-methyladenosine in isoforms of the same gene in a cell-type-specific manner.