Methods in the spotlight

Here is a selection of interesting new methods published in the literature as curated by Nature Methods editors. Stay tuned for our July issue to read Research Highlights on a few of our top picks this month.

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The Nature Methods editorial team gets together each month to pick interesting new methods developments that are published in other journals for the Research Highlights section. Unfortunately, we can't highlight all the great methods being developed. Below are a few exciting papers that we couldn't feature in our upcoming issue.

BIOCHEMISTRY AND PROTEOMICS

Hartrampf et al. Synthesis of proteins by automated flow chemistry. Science 368, 980-987 (2020).

This paper reports a method for chemical synthesis of proteins. Solid-phase peptide synthesis is only feasible for peptides shorter than 50 amino acids and can be quite slow. Here, the authors report an automated flow cytometry-based method that can synthesize much longer chains with a cycle time of ~2.5 min per amino acid. In the paper, they show that they can build barstar (90 amino acids) and sortase A (164 amino acids) in 3.5 and 6.5 hours, respectively.

Müller J.B. et al. The proteome landscape of the kingdoms of life. Nature 582, 592-596 (2020).

This paper presents a large scale cross-species comparative proteomic analysis. The authors have looked at 100 diverse species, 2 million peptides and some 340,000 stringent protein identifications in a standardized manner. The workflow involved peptide separation using a chip-based chromatographic method, that they report to be highly reproducible. They use these 2 million peptides and their retention times to train a deep learning-based model, with an interpretable attention layer. They demonstrate the utility by predicting retention times for peptides from organisms not part of the 100 previously analyzed ones and by experimentally confirming them.

Jelcic M. et al. A Photo-clickable ATP-Mimetic Reveals Nucleotide Interactors in the Membrane Proteome. Cell Chem. Biol. https://doi.org/10.1016/j.chembiol.2020.05.010 (2020).

A minimally invasive photoaffinity ATP (mipATP) allows improved mapping of ATP-protein interactions. mipATP is compact and retains the calcium signaling responses of ATP in vitro and in vivo.

Ruggeri F.S. et al. Single molecule secondary structure determination of proteins through infrared absorption nanospectroscopy. Nat. Commun. 11, 2945 (2020).

Off-resonance, low power and short pulse infrared nanospectroscopy (ORS-nanoIR) allows the acquisition of infrared absorption spectra and chemical maps at the single-molecule level, and enables the accurate determination of the secondary structure of single proteins.

GENOMICS AND GENETICS

Javdan B. et al. Personalized Mapping of Drug Metabolism by the Human Gut Microbiome. Cell 181, 1661–1679 (2020).

The human gut microbiota contains hundreds of bacterial species which are known to play an important role in human health and disease. Javdan et al. describe an experimental framework to study drug metabolism in the human gut microbial community. They develop an ex vivo culturing system to grow the microorganisms from a specific microbiome sample and use metagenomic screens to study genes involving metabolic events, thus offering an approach to explore the drug-microbiome interactions in gut microbial community. 

Sas-Chen A. et al. Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping. Nature https://doi.org/10.1038/s41586-020-2418-2 (2020).

The occurrence of cytidine acetylation or N4-acetylcytidine (ac4C) has been studied in eukaryotes such as humans and yeast. Yet, quantitatively profiling ac4C at single-nucleotide resolution is lagging. Sas-Chen et al. describe ac4C-seq, a transcriptome-wide, quantitative approach to map ac4C at base resolution. In ac4C-seq, ac4C is converted to a reduced nucleobase that leads to a C>T misincorporation, thus offering a way to detect ac4C during sequencing. Ac4C-seq enables to profile ac4C across eukaryotes and archaea, as well as different RNA species.

Arbab M. et al. Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning. Cell https://doi.org/10.1016/j.cell.2020.05.037 (2020).

A machine learning model trained on target library assay data predicts editing efficiency and patterns of cytosine and adenine base editors.

Zook J.M. et al. A robust benchmark for detection of germline large deletions and insertions. Nat. Biotechnol. https://doi.org/10.1038/s41587-020-0538-8 (2020).

A benchmark set of germline large deletions and insertions facilitates assessment of sequencing and computational methods.

CELL BIOLOGY AND STEM CELLS

Takeishi K. et al. Assembly and Function of a Bioengineered Human Liver for Transplantation Generated Solely from Induced Pluripotent Stem Cells. Cell Reports 31, 107711 (2020).

Takeishi et al. generated implantable mini human livers by differentiating the different cellular components of the liver from human induced pluripotent stem cells in vitro. These cells were used to repopulate decellularized rat liver scaffolds and shown to be functional when transplanted into immunodeficient rats.

IMAGING AND MICROSCOPY

Schubert M. et al. Monitoring contractility in cardiac tissue with cellular resolution using biointegrated microlasers. Nat. Photonics 14, 452–458 (2020).

The introduction of intracellular microlasers into cardiac cells enables the single-cell resolution imaging of their contractility. This technique enabled tracking of contractility in live zebrafish and rat heart tissue.​

IMMUNOLOGY

Mehta N.K. et al. Pharmacokinetic tuning of protein–antigen fusions enhances the immunogenicity of T-cell vaccines. Nat. Biomed. Eng. 4, 636–648 (2020).

Mehta et al. demonstrated that fusing peptide vaccines with the carrier protein transthyretin could enhance the immunogenicity of a T cell vaccine. Altering the biodistribution of the vaccine ensured better antigen accumulation and uptake in primary lymphoid organs, thus improving vaccine-induced T cell responses.

Ahl P.J. et al. Met-Flow, a strategy for single-cell metabolic analysis highlights dynamic changes in immune subpopulations. Commun Biol 3, 305 (2020).

Ahl et al. developed Met-Flow, a multiparametric FACS-based assay that captures the metabolic state of immune cells by detecting the protein expression of critical enzymes. Using dimensionality reduction methods, they showed that metabolic state alone could be used to broadly classify immune cells into subtypes, thus linking metabolic phenotype to immune cell function.

Bresser K. et al. A mouse model that is immunologically tolerant to reporter and modifier proteins. Commun Biol 3, 273 (2020).

The introduction of exogenous reporter genes into adult mice can result in activation of the immune system as the expressed reporters can be recognized as foreign. This immune response is avoided in transgenic mice harboring a transgene that consists of shuffled fragments of commonly used reporters. The resulting immunological tolerance facilitates for example the adoptive transfer of fluorescently labeled T cells.

NEUROSCIENCE

Fenno L.E. et al. Comprehensive Dual- and Triple-Feature Intersectional Single-Vector Delivery of Diverse Functional Payloads to Cells of Behaving Mammals. Neuron https://doi.org/10.1016/j.neuron.2020.06.003 (2020).

The Deisseroth lab has generated a toolbox of AAV vectors for the expression of various opsins, calcium indicators and fluorescent proteins under dual or triple intersectional control. Expression of effectors is dependent on Cre, Flp and in some instances VCre, allowing restricted expression in subpopulations of cell types.

Nina Vogt

Senior Editor, Nature Methods

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