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 August issue.
BIOCHEMISTRY AND PROTEOMICS
Mäeots, M.-E. et al. Modular microfluidics enables kinetic insight from time-resolved cryo-EM. Nat. Commun. 11, 3465 (2020).
A method to prepare samples for time-resolved cryo-EM. This microfluidic device features a 3D-mixing unit and variable mixing and incubation times to automate sample vitrification. The incubation times can range from ten to thousands of milliseconds, to enrich the intermediate states on cryo-EM grids.
Huang, T. et al. MSstatsTMT: Statistical detection of differentially abundant proteins in experiments with isobaric labeling and multiple mixtures, Mol. Cell. Proteomics https://doi.org/10.1074/mcp.RA120.002105 (2020).
MSstatsTMT is an extension of the MSstats, an R package for statistical analysis of mass spectrometry-based proteomics data. It allows for statistical relative quantification of differentially abundant proteins in mass spectrometry experiments with TMT labeling.
Heidenreich M. et al. Designer protein assemblies with tunable phase diagrams in living cells. Nat. Chem. Biol. https://doi.org/10.1038/s41589-020-0576-z (2020).
This paper reports a two-protein system to reconstruct phase diagram in living cells, which can be achieved by modulating the interaction affinities of the two proteins and thus their phase behaviors in yeast cells.
GENOMICS AND GENETICS
Song M. et al. Sequence-specific prediction of the efficiencies of adenine and cytosine base editors. Nat. Biotechnol. https://doi.org/10.1038/s41587-020-0573-5 (2020).
In this paper, the authors profiled the editing outcomes of adenine base editors (ABEs) and cytosine base editors (CBEs) at over thirteen thousand target sequences in human cells. The resulting datasets lead to a deep learning model that can predict the efficiencies and outcomes of ABE and CBE editing at target sequences.
Kurt I.C. et al. CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells. Nat. Biotechnol. https://doi.org/10.1038/s41587-020-0609-x (2020).
Zhao D. et al. Glycosylase base editors enable C-to-A and C-to-G base changes. Nat. Biotechnol. https://doi.org/10.1038/s41587-020-0592-2 (2020).
The Joung group and the Zhang group independently report C-to-G base editors. They achieve C-to-G editing by fusing Cas9 nickase with uracil-DNA glycosylase and cytidine deaminase. The installation of C-to-G editing provides additional possibilities for amino acid substitutions that were not possible with CBEs or ABEs.
Zhang Z. et al. Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability. Nat. Genet. https://doi.org/10.1038/s41588-020-0644-z (2020).
mRNA N6-methyladenosine (m6A) modifications regulate various biological processes. Zhang et al. perform QTL mapping to identify genetic variants associated with m6A levels in lymphoblastoid cell lines, and find m6A QTLs contribute to the heritability of complex traits.
Bost P. et al. Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients. Cell 181, 1475–1488 (2020).
A virus infection can lead to widespread transcriptomic changes in host cells. Bost et al. develop Viral-Track, a computational method for analyzing single-cell RNA-seq data from virus-infected cells and bystander cells. They apply it to samples from COVID-19 patients, and find immune responses caused by SARS-CoV-2 infection.
CELL BIOLOGY AND STEM CELLS
El-Nachef D. et al. A Rainbow Reporter Tracks Single Cells and Reveals Heterogeneous Cellular Dynamics among Pluripotent Stem Cells and Their Differentiated Derivatives. Stem Cell Reports 15, 226-241 (2020).
El-Nachef et al. have transduced human pluripotent stem cells (hPSCs) with a Cre-inducible rainbow reporter to fluorescently label single cells with 18 unique colors. Rainbow hPSCs could be tracked at a single cell level to reveal unique cell proliferation and migration patterns.
Zhou J. et al. Infection of bat and human intestinal organoids by SARS-CoV-2. Nat. Med. 26, 1077-1083 (2020).
Zhou et al. have developed the first bat intestinal organoids to demonstrate sustained SARS-CoV-2 infection and replication in bat cells. In addition, they have used human enteroids to analyze the possibility of a gastrointestinal route of infection and to shed light on reports of gastrointestinal symptoms in a subset of COVID-19 patients.
IMAGING AND MICROSCOPY
Kounatidis I. et al. 3D Correlative cryo-structured illumination fluorescence and soft X-ray microscopy elucidates reovirus intracellular release pathway. Cell 182, 515–530 (2020).
A combination of cryo-structured illumination microscopy and soft X-ray tomography allows correlated 3D imaging of cellular ultrastructure and fluorescently labeled proteins. The correlative method was used to study reovirus release from intracellular vesicles, and the instrument is available at the Diamond Light Source.
Hou S. et al. Real-time 3D single molecule tracking. Nat. Commun. 11, 3607 (2020).
3D single-molecule active real-time tracking (3D-SMART) enables tracking of single fluorophores freely moving in solution for minutes at a time. 3D-SMART works by actively tracking a fluorophore as it moves through active feedback with the hardware and software. The method was fast enough to track fluorophores moving freely in 90% glycerol and was able to capture active transcription on single freely diffusing DNA.
Yang X. et al. Mitochondrial dynamics quantitatively revealed by STED nanoscopy with an enhanced squaraine variant probe. Nat. Commun. 11, 3699 (2020).
An enhanced squaraine dye called MitoESq-635 was developed for bright and photostable labeling of mitochondria. Time-lapse imaging of labeled mitochondria in mammalian cells using STED microscopy revealed high resolution images of mitochondrial cristae, and revealed fusion and fission events.
Guo M. et al. Rapid image deconvolution and multiview fusion for optical microscopy. Nat. Biotechnol. https://doi.org/10.1038/s41587-020-0560-x (2020).
Three approaches are described to improve the speed of image deconvolution and computational fusion of multiple views of the same sample. In the first, an ‘unmatched back projector’ accelerates deconvolution ten-fold relative to Richard-Lucy deconvolution. In the second, GPU based processing enhances 3D image registration 10-100-fold relative to CPU processing. Finally, a deep learning-based approach is used to further accelerate deconvolution.
Dou G. et al. Chimeric apoptotic bodies functionalized with natural membrane and modular delivery system for inflammation modulation. Sci. Adv. https://advances.sciencemag.org/content/6/30/eaba2987 (2020).
Apoptotic bodies (ABs) are exosomes released by cells on the verge of apoptosis and are known to have immune modulatory properties. Here, Dou et al. have created chimeric apoptotic bodies by fusing ABs to a nanoparticle delivery system. Chimeric ABs are able to polarize M2 macrophages by delivering anti-inflammatory reagents to the site of inflammation, thereby regulating the immune response.
Verschueren E. et al. The Immunoglobulin Superfamily Receptome Defines Cancer-Relevant Networks Associated with Clinical Outcome. Cell 182, 329-344 (2020).
Verschueren et al. have generated an interactome by mapping the receptor-ligand binding between single transmembrane receptors (STM) and immunoglobulin superfamily proteins (IgSF) and identified over 440 novel interactions. This is a rich resource that allows for the analyses of protein interactions governing diseases like cancer, thus opening up avenues for exploration of disease pathology and novel therapeutic approaches.
Shemesh O.A. et al. Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator. Neuron https://www.cell.com/neuron/fulltext/S0896-6273(20)30398-6 (2020).
Calcium imaging with genetically encoded calcium indicators can be hampered by crosstalk from expression in the neuropil. Shemesh et al. generated soma-targeted versions of GCaMP6f and GCaMP7f, which avoids this crosstalk as shown in zebrafish and mouse brain.
Abdelfattah A.S. et al. A general approach to engineer positive-going eFRET voltage indicators. Nat Commun. 11, 3444 (2020).
Genetically encoded or hybrid voltage sensors such as e.g. Ace2N-mNeon or Voltron report action potentials or depolarization with a decrease in their FRET signal. Abdelfattah et al. present versions of these voltage sensors with inverted polarity. Their Positron sensor is based on Voltron but responds to depolarization with an increase in FRET.
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