Volume 17 Issue 10, October 2022

Fibroblast cell forming filopodia on nanopatterns

Scanning electron microscope image (pseudo-color) of a fibroblast cell forming filopodia along nanofibers functionalized by the integrin-binding peptide Arg–Gly–Asp (RGD). The nanopatterns are arrays of 20-nm-wide lines with 80-nm center-to-center distance in each line pair. Functionalization of ligands on titanium nanopatterns enables super-resolution fluorescence microscopy to study cell–ligand interactions at the molecular scale.

See Jain et al.

Image: Haogang Cai, New York University Grossman School of Medicine. Cover design: S. Harris

Perspectives

Prototype mouse models for researching SEND-based mRNA delivery and gene therapy

In this Perspective, the authors propose genetically engineered mouse models to further the understanding and use of a recently discovered tool, selective endogenous encapsidation for cellular delivery via virus-like particles, in gene delivery and gene therapy applications.

Channabasavaiah B. Gurumurthy
Rolen M. Quadros
Masato Ohtsuka
Perspective 03 Aug 2022
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Protocol Extensions

Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control

This extension of the TCP-seq protocol describes procedures for selective profiling of 40S and 80S ribosome subpopulations bound by a factor of interest, permitting detailed studies of the different stages of translation in mammalian and yeast cells.

Susan Wagner
Jonathan Bohlen
Aurelio A. Teleman
Protocol Extension 22 Jul 2022

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Protocols

Scalable tissue labeling and clearing of intact human organs

This protocol describes labeling, clearing, imaging and cellular-level three-dimensional image reconstruction of intact human organs achieved with the help of a novel tissue clearing and labeling technology and a commercially available microscope.

Hongcheng Mai
Zhouyi Rong
Ali Ertürk
Protocol 20 Jul 2022
A rapid screening platform to coculture bacteria within tumor spheroids

Bacteria spheroid coculture allows long-term growth of bacteria in the hypoxic, necrotic core of tumor spheroids. This enables the study of bacteria–tumor interactions and rapid development of engineered microbial therapies.

Tetsuhiro Harimoto
Dhruba Deb
Tal Danino
Protocol 29 Jul 2022
Nanocarriers based on bacterial membrane materials for cancer vaccine delivery

This protocol details the construction of two types of nanocarrier based on bacterial membrane materials and their use in vaccine delivery to create cancer nanovaccines.

Xiao Zhao
Ruifang Zhao
Guangjun Nie
Protocol 25 Jul 2022
Ligand functionalization of titanium nanopattern enables the analysis of cell–ligand interactions by super-resolution microscopy

Receptor-mediated signaling occurs at nanoscale. Understanding this requires nanopatterning and imaging techniques compatible at this scale. Rapid functionalization of Ti nanopatterns allows nanoscale visualization of early steps in cell signaling.

Kashish Jain
Pakorn Kanchanawong
Rishita Changede
Protocol 27 Jul 2022
High-throughput proteomic sample preparation using pressure cycling technology

High-throughput lysis and proteolytic digestion of biopsy-level tissue specimens is a major bottleneck for clinical proteomics. This protocol describes pressure cycling technology (PCT)-assisted sample preparation of biopsy tissues.

Xue Cai
Zhangzhi Xue
Tiannan Guo
Protocol 05 Aug 2022
I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction

A protocol is described for predicting the structures and functions of multi-domain proteins using the freely available deep-learning-based web platform I-TASSER-MTD.

Xiaogen Zhou
Wei Zheng
Yang Zhang
Protocol 05 Aug 2022
Single-cell RNA and protein profiling of immune cells from the mouse brain and its border tissues

This protocol enables single-cell multi-omic analysis of the mouse brain immune compartment to explore immune cell heterogeneity and activation in the healthy and diseased brain, using a workflow based on HD flow cytometry, scRNA-seq and CITE-seq.

Isabelle Scheyltjens
Hannah Van Hove
Kiavash Movahedi
Protocol 05 Aug 2022
Single-crystal structure determination of nanosized metal–organic frameworks by three-dimensional electron diffraction

Metal–organic frameworks have a well-defined pore architecture and tunable functional characteristics based on their structure. This protocol explains how to determine the structure of nano- (submicron-)sized crystals by three-dimensional electron diffraction.

Taimin Yang
Tom Willhammar
Zhehao Huang
Protocol 27 Jul 2022

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Volume 17 Issue 10, October 2022

Fibroblast cell forming filopodia on nanopatterns

Perspectives

Prototype mouse models for researching SEND-based mRNA delivery and gene therapy

Protocol Extensions

Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control

Protocols

Scalable tissue labeling and clearing of intact human organs

A rapid screening platform to coculture bacteria within tumor spheroids

Nanocarriers based on bacterial membrane materials for cancer vaccine delivery

Ligand functionalization of titanium nanopattern enables the analysis of cell–ligand interactions by super-resolution microscopy

High-throughput proteomic sample preparation using pressure cycling technology

I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction

Single-cell RNA and protein profiling of immune cells from the mouse brain and its border tissues

Single-crystal structure determination of nanosized metal–organic frameworks by three-dimensional electron diffraction

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