The Invention Science Fund I LLC

Massachusetts Institute of Technology

Elwha LLC

Leland Stanford Junior University

University of Alberta

Searete LLC

Gearbox LLC

Harvard College

Georgia Tech Research Corporation

Beth Israel Deaconess Medical Center, Inc.

Elemind Technologies, Inc.

Nuvu LLC

Wake Forest University

Deep Science, LLC

Eos Neuroscience, Inc.

Edward Stuart Boyden

Roderick A Hyde

Eric Leuthardt

Lowell L Wood, Jr

Nathan P Myhrvold

Dennis James Rivet, Ii

Muriel Y Ishikawa

Michael A Smith

Elizabeth A Sweeney

Clarence T Tegreene

Victoria Y H Wood

Thomas A Weaver

Charles Whitmer

Edward K Y Jung

Daniel B Cook

Robert Samuel Langer

Gregory J Della Rocca

Jordin T Kare

Daniel Hawkins

Parag Jitendra Parikh

Terence Myckatyn

Joshua S Shimony

Robert W Lord

Stephen L Malaska

Karl A Deisseroth

Brian Yichiun Chow

Nathan Klapoetke

Mahalaxmi Gita Bangera

Fei Chen

Yongku Peter Cho

Paul G Allen

Asmamaw T Wassie

Hon Wah Chin

Ralph G Dacey, Jr

Joshua L Dowling

Gane Ka-Shu Wong

Nir Grossman

Feng Zhang

Colin Derdeyn

Adam H Marblestone

Paul Warren Tillberg

Shahar Alon

Gregory Zipfel

Paul Santiago

Todd J Stewart

Glenn B Foster

Sharon L Wolda

W Daniel Hillis

Evan R Daugharthy

Leif T Stordal

Ruixuan Gao

David Wang

Amy S Chuong

Chih-Chieh Yu

Bran Ferren

George M Church

David Bazeley Tuckerman

William David Duncan

Jesse R Cheatham, Iii

Clifton Fonstad, Jr

Linyi Gao

David Bono

Anthony Zorzos

Katarzyna P Adamala

Christopher Rowlands

Samuel Gordon Rodriques

Daniel Alberto Martin-Alarcon

Moshe Ben Ezra

Young Gyu Yoon

Or A Shemesh

Changyang Linghu

Xue Han

Suhasa Bangalore Kodandaramaiah

Daniel Masao Estandian

Andrew C Payne

Yongxin Zhao

Alexi Georges Choueiri

Michael Baym

Craig Richard Forest

Roy P Diaz

Ho-Jun Suk

Jorg Scholvin

Kiryl Piatkevich

Giovanni Talei Franzesi

Jacob Bernstein

Brian Douglas Allen

Aimei Yang

Tony S Pan

Alistair K Chan

Robert C Petroski

Li-Huei Tsai

Adam Ezra Cohen

Mark Andrew Skylar-Scott

Daniel Hochbaum

Anthony James Martorell

Jonathan Scheiman

Daniel Oran

Jason Daniel Buenrostro

Jae-Byum Chang

Christian T Wentz

The present invention provides biological samples of interest that have been iteratively expanded in a method referred to herein as iterative direct expansion microscopy (id-ExM). In the id-ExM method, biological samples of interest are permeated with a swellable material that results in the sample becoming embedded in the swellable material, and then the sample can be expanded isotropically in three dimensions. The process of iteratively expanding the samples can be applied to expand samples one or more additional times such that, for example, a 5-fold expanded sample can be expanded again to achieve high expansion factors, for example, 20× to 100× or more linear expansion.

Iterative direct expansion microscopy

The present description provides methods, assays and reagents useful for sequencing proteins. Sequencing proteins in a broad sense involves observing the plausible identity and order of amino acids, which is useful for sequencing single polypeptide molecules or multiple molecules of a single polypeptide. In one aspect, the methods are useful for sequencing multiple polypeptides. The methods and reagents described herein can be useful for high resolution interrogation of the proteome and enabling ultrasensitive diagnostics critical for early detection of diseases.

Single-molecule protein and peptide sequencing

The invention, in some aspects, relates to polypeptide molecules and their encoding nucleic acid molecules and use of such molecules to direct and localize sensor molecules in the soma of cells in which they are expressed. Compositions of the invention may be delivered to cells and subjects and used in methods to determine activity in cells in which they are expressed.

Cell body targeted sensors

The invention, in some aspects relates to compositions and methods for altering cell activity and function and the introduction and use of light-activated ion channels.

Channelrhodopsins for optical control of cells

The present invention provides compositions and methods that allow lipid membranes to be imaged optically at nanoscale resolution via a lipid-optimized form of expansion microscopy, also referred to as membrane expansion microscopy (mExM). mExM, via a post-expansion antibody labeling protocol, enables protein-lipid relationships to be imaged in organelles such as mitochondria, the endoplasmic reticulum, the nuclear membrane, and the Golgi apparatus. mExM may be of use in a variety of biological contexts, including the study of cell-cell interactions, intracellular transport, and neural connectomics.

Membrane probes for expansion microscopy

The invention encompasses hydrogels, monomer precursors of the hydrogels, methods for the preparation thereof, and methods of use therefor. The linking of monomers can take place using non-radical, bioorthogonal reactions such as copper-free click-chemistry.

Swellable and structurally homogenous hydrogels and methods of use thereof

The invention provides a method for preparing an expanded cell or tissue sample suitable for microscopic analysis. Expanding the sample can be achieved by binding, e.g., anchoring, key biomolecules to a DMAA-TF polymer network and swelling, or expanding, the polymer network, thereby moving the biomolecules apart as further described herein. As the biomolecules are anchored to the polymer network isotropic expansion of the polymer network retains the spatial orientation of the biomolecules resulting in an expanded, or enlarged, sample.

Dimethylacrylamide (DMAA) hydrogel for expansion microscopy (ExM)

A method for diagnosing cancer in an expanded biological tissue sample of a patient comprising providing at least one sample image of the expanded biological tissue sample; providing a computer configured to analyze the sample; analyzing, with the computer, the sample detect and segment nuclei; calculating, with the computer, molecular characteristics of those nuclei; and determining, with the computer, a diagnosis of cancer of the sample by comparing the sample with a benign normal tissue reference.

Methods for diagnosing neoplastic lesions

The invention, in part, includes methods of single molecule protein sequencing that include using weak binding spectra in the amino acid identification.

Single molecule peptide sequencing methods

The invention provides a method for preparing an expanded renal (kidney) tissue sample suitable for microscopic analysis. Expanding the kidney sample can be achieved by binding, e.g., anchoring, key biomolecules to a polymer network and swelling, or expanding, the polymer network, thereby moving the biomolecules apart as further described herein. As the biomolecules are anchored to the polymer network, isotropic expansion of the polymer network retains the spatial orientation of the biomolecules resulting in an expanded, or enlarged, kidney sample.

Methods for examining podocyte foot processes in human renal samples using conventional optical microscopy

The invention provides a method for preparing an expanded biological specimen suitable for microscopic analysis. Expanding the biological sample can be achieved by anchoring biomolecules to a polymer network and swelling, or expanding, the polymer network, thereby moving the biomolecules apart as further described below. As the biomolecules are anchored to the polymer network isotropic expansion of the polymer network retains the spatial orientation of the biomolecules resulting in an expanded, or enlarged, biological specimen.

Multiplexed expansion (MultiExM) pathology

The invention, in some aspects, relates to the preparation and use of signaling reporter islands (SiRIs) in single cells. Compositions of the invention that produce SiRIs can be delivered to a cell resulting in the presence of one or more SiRIs in the cell. Methods of the invention include detecting signals generated by elements in the SiRIs in a cell and use of the detected signals to determine and analyze simultaneous physiological processes within the cell, or cells.

Methods for simultaneous measurement of multiple biological signals from spectrally identical fluorescent reporters

The present invention provides compositions and methods for the selective silencing of neurons in pain pathway by using a combination of inhibitory light-sensitive protein gene transfer and wavelength specific illumination.

Methods and compositions for decreasing chronic pain

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Chestnut Hill, MA, United States of America

Edward Stuart Boyden