The Nature Methods editorial team gets together each month to pick their favorite methods papers for the Research Highlights and In Brief section. We aim to provide for our readers a balanced selection across the different fields that Nature Methods covers. Below are exciting papers that we unfortunately couldn't highlight in our April issue.
Almagro Armenteros et al. SignalP 5.0 improves signal peptide predictions using deep neural networks
SignalP 5.0 is a deep neural network-based method for predicting signal peptides across all domains of life, with improved prediction performance over previous tools.
A combination of genetic code expansion, Staudinger reduction, and sortase-mediated transpeptidation enables inducible ubiquitylation of proteins for functional studies with temporal control.
A broad range of complex carbohydrates can be made by enzyme-mediated synthesis using an automated catch-and-release platform.
Almeida et al. A new genomic blueprint of the human gut microbiota
More than 90,000 metagenome-assembled genomes from human gut microbiomes were reconstructed, revealing close to 2,000 uncultured bacterial species, in addition to culturable bacteria.
CATCH is a computational tool for designing oligonucleotide probe sets to improve nucleic acid capture when analyzing diverse microbial taxa. Application of the tool preserves sample diversity in metagenomics sequencing.
Fluorescence lifetime imaging (FLIM) can be applied to study concentration-dependent biocondensation in living cells. Here, cyclic changes in protein concentration within major nuclear organelles and heterochromatin domains could be observed.
The MicroColonyChip facilitates rapid and high-throughput colony forming assays and is applied here to assess radiosensitivity and chemosensitivity.
A low-cost super-hemispherical solid immersion lens (superSIL) enables straightforward multicolor, high-resolution localization microscopy at cryogenic conditions.
Clickable, azobenzene-containing ceramides, caCers, are used for optical control of sphingolipid production in cells.
CPX is a small photoconvertible probe that can be "clicked" to biological molecules via an azide-alkyne cycloaddition. It can be used to track molecules, complexes and even compartments.
A contactless acoustic gradient force trap for sample confinement can help overcome the restrictions of sample immobilisation and mounting in light sheet microscopy.
To facilitate connectivity studies in the zebrafish brain, a resource of more than 50 Cre lines for intersectional mapping have been created, and expression patterns are available at the Zebrafish Brain Browser.
Efficient photoswitches for isomerization under two-photon conditions are developed and applied to regulate light-gated glutamate receptors in hippocampal slices and in C. elegans.
A split botulinum neurotoxin has been rendered photoactivatable with the help of the CRY2-CIBN photodimerization tool. The light-inducible tool has been used to inhibit neurotransmission in brain slices as well as in C. elegans.
We hope that you enjoy this selection of methods!