Professors Jack Strominger, Kit Parker, David Weitz, David Liu, George Church, Adam Cohen, Darren Higgins, Jene A. Golovchenko, and Mikhail Lukin were among the faculty members issued U.S. patents this June. The patents include:

Synthetic peptides and methods of use for autoimmune disease therapies
U.S. Patent 9,066,905 (June 30, 2015)
Jack L. Strominger and Masha Fridkis-Hareli

The invention provides heteropolymer compositions and peptide compositions, and methods of making and using therapeutic compositions comprising amino acid heteropolymers for treatment of a subject for an autoimmune or an inflammatory disease, the heteropolymer compositions made by solid state synthesis. The invention also provides kits for assaying binding of a composition to a water-soluble MHC protein.

Glycated CD59 peptides, their preparation, and uses thereof
U.S. Patent 9,068,006 (June 30, 2015)
Jose A. Halperin and Michael Chorev

The present invention provides glycated Amadori products of the CD59 peptide and fragments thereof to be used as tools and among methods for the diagnosis and prognosis of pre-diabetes and diabetes. Certain aspects of the invention include glycated Amadori products of CD59 and fragments thereof to be used for the generation of antibodies and antibody fragments. Still other aspects of the invention include methodologies for the preparation of glycated Amadori products of CD59, fragments thereof, the inventive antibodies, and antibody fragments.

Boundary conditions for the arrangement of cells and tissues
U.S. Patent 9,068,168 (June 30, 2015)
Adam W. Feinberg, Kevin Kit Parker, Po-Ling Kuo, and Chin-Lin Guo

The present invention relates to the arrangement of one or more cells in a medium or on a substrate through the use of boundary conditions, which are changes in local environment compared to the medium or substrate alone or cause an alteration of cell response upon interaction of a cell with the boundary condition.

Methods for correcting presenilin point mutations
U.S. Patent 9,068,179 (June 30, 2015)
David R. Liu and Alexis Christine Komor

Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids, including editing a nucleic acid encoding a mutant Presenilin1 protein to correct a point mutation associated with a disease or disorder, e.g., with familial Alzheimer's disease. The methods provided are useful for correcting a PSEN1 point mutation within the genome of a cell or subject, e.g., within the human genome. In some embodiments, fusion proteins of Cas9 and nucleic acid editing enzymes or enzyme domains, e.g., deaminase domains, are provided. In some embodiments, reagents and kits for the generation of targeted nucleic acid editing proteins, e.g., fusion proteins of Cas9 and nucleic acid editing enzymes or domains, are provided.

Assay and other reactions involving droplets
U.S. Patent 9,068,210 (June 30, 2015)
Jeremy Agresti, Liang-Yin Chu, David A. Weitz, Jin-Woong Kim, Amy Rowat, Morten Sommer, Gautam Dantas, and George Church

The present invention generally relates to droplets and/or emulsions, such as multiple emulsions. In some cases, the droplets and/or emulsions may be used in assays, and in certain embodiments, the droplet or emulsion may be hardened to form a gel. In some aspects, a heterogeneous assay can be performed using a gel. For example, a droplet may be hardened to form a gel, where the droplet contains a cell, DNA, or other suitable species. The gel may be exposed to a reactant, and the reactant may interact with the gel and/or with the cell, DNA, etc., in some fashion. For example, the reactant may diffuse through the gel, or the hardened particle may liquefy to form a liquid state, allowing the reactant to interact with the cell. As a specific example, DNA contained within a gel particle may be subjected to PCR (polymerase chain reaction) amplification, e.g., by using PCR primers able to bind to the gel as it forms. As the DNA is amplified using PCR, some of the DNA will be bound to the gel via the PCR primer. After the PCR reaction, unbound DNA may be removed from the gel, e.g., via diffusion or washing. Thus, a gel particle having bound DNA may be formed in one embodiment of the invention.

Manipulation of fluids, fluid components and reactions in microfluidic systems
U.S. Patent 9,068,699 (June 30, 2015)
Seth Fraden, Hakim Boukellal, Yanwei Jia, Seila Selimovic, Amy Rowat, Jeremy Agresti, and David A. Weitz

Microfluidic structures and methods for manipulating fluids, fluid components, and reactions are provided. In one aspect, such structures and methods can allow production of droplets of a precise volume, which can be stored/maintained at precise regions of the device. In another aspect, microfluidic structures and methods described herein are designed for containing and positioning components in an arrangement such that the components can be manipulated and then tracked even after manipulation. For example, cells may be constrained in an arrangement in microfluidic structures described herein to facilitate tracking during their growth and/or after they multiply.

Droplet creation techniques
U.S. Patent 9,056,289 (June 16, 2015)
David A. Weitz and Adam R. Abate

The present invention is generally related to systems and methods for producing droplets. The droplets may contain varying species, e.g., for use as a library. In some cases, at least one droplet is used to create a plurality of droplets, using techniques such as flow-focusing techniques. In one set of embodiments, a plurality of droplets, containing varying species, can be divided to form a collection of droplets containing the various species therein. A collection of droplets, according to certain embodiments, may contain various subpopulations of droplets that all contain the same species therein. Such a collection of droplets may be used as a library in some cases, or may be used for other purposes.

Scale-up of flow-focusing microfluidic devices
U.S. Patent 9,056,299 (June 16, 2015)
Mark Romanowsky, Adam R. Abate, and David A. Weitz

Parallel uses of microfluidic methods and devices for focusing and/or forming discontinuous sections of similar or dissimilar size in a fluid are described. In some aspects, the present invention relates generally to flow-focusing-type technology, and also to microfluidics, and more particularly parallel use of microfluidic systems arranged to control a dispersed phase within a dispersant, and the size, and size distribution, of a dispersed phase in a multi-phase fluid system, and systems for delivery of fluid components to multiple such devices.

Optogenetic probes for measuring membrane potential
U.S. Patent 9,057,734 (June 16, 2015)
Adam E. Cohen, Joel M. Kralj, and Adam D. Douglass

The invention provides methods, cells and constructs for optical measurement of membrane potential. These methods can be used in cells that are not accessible to presently available methods using electrodes. The methods can be directed to, for example, high-throughput drug screening assays to determine agents that can affect membrane potential of a target cell.

Compositions for and methods of identifying antigens
U.S. Patent 9,051,564 (June 9, 2015)
Darren E. Higgins, Michael N. Starnbach, Todd Gierahn, and Nadia R. Roan

Replicable libraries having discrete members in defined locations for screening for antigens to a pathogenic organism are provided. Also provided are methods for using such libraries as well as a specific antigen, CT788, which induces T-cell activation during a Chlamydia infection.

Two-dimensional coupled resonator optical waveguide arrangements and systems, devices, and methods thereof
U.S. Patent 9,052,448 (June 9, 2015)
Mohammad Hafezi, Jacob Taylor, Eugene Demler, and Mikhail Lukin

Two-dimensional coupled resonator optical waveguide arrangements and systems, devices, and methods thereof. Networks of coupled resonator optical waveguides are arranged so as to exploit topological properties of these optical networks. Such arrangement affords topological protection against disorders or perturbations in the network that may hinder or block photon flow. As a result of a disorder, photons traversing along edge states of the array are rerouted based on the disorder or perturbation. Photon routing in the network is accordingly protected against disorder or defects.

Characterization of individual polymer molecules based on monomer-interface interactions
U.S. Patent 9,046,483 (June 2, 2015)
Timothy J. Denison, Alexis Sauer-Budge, Jene A. Golovchenko, Amit Meller, Eric Brandin, and Daniel Branton

The invention relates to a method for characterizing a target polynucleic acid by providing a surface containing a channel of a dimension sufficient to allow sequential monomer-by-monomer passage of a single-stranded polynucleic acid, but not of a double-stranded polynucleic acid; providing a source of hybridized target polynucleic acid at the surface; inducing passage of the target polynucleic acid through the channel, whereby the target polynucleic acid undergoes base pair separation (melts) prior to its passage; and making one or more measurements over time as the target polynucleic acid moves relative to the channel yielding data suitable to determine a monomer-dependent characteristic of the target polynucleic acid.