Abstract: This application describes systems and methods for assaying micro-objects in a microfluidic device. These methods include contacting a reagent with a micro-object by introducing a reagent in a first fluidic medium to a flow region of a microfluidic device, wherein the microfluidic device comprises the flow region and a chamber comprising a proximal opening fluidically connecting the chamber to the flow region, diffusing the reagent from the flow region into the chamber; introducing a micro-object into the flow region of the microfluidic device, and diffusing the reagent from the chamber to the flow region to contact the reagent with the micro-object within the flow region. Other embodiments are described.

Abstract: In biosciences and related fields, it can be useful to study cells in isolation so that cells having unique and desirable properties can be identified within a heterogenous mixture of cells. Processes and methods disclosed herein provide for encapsulating cells within a microfluidic device and assaying the encapsulated cells. Encapsulation can, among other benefits, facilitate analyses of cells that generate secretions of interest which would otherwise rapidly diffuse away or mix with the secretions of other cells.

Abstract: In situ-generated microfluidic isolation structures incorporating a solidified polymer network, methods of preparation and use, compositions and kits therefor are described. The ability to introduce in real time, a variety of isolating structures including pens and barriers offers improved methods of micro-object manipulation in microfluidic devices. The in situ-generated isolation structures may be permanently or temporarily installed.

Abstract: Methods, systems, and kits for determining a level of dissolved oxygen within a microfluidic device are provided. The microfluidic device can be suitable for cell culture. The methods, systems, and kits can further be used to determine a level of oxygen consumption in a population of biological micro-objects. In particular, the methods, systems, and kits of the present disclosure rely on flowing a fluidic medium containing a dye and a supplied partial pressure of oxygen into the microfluidic device for a period of time, wherein fluorescence emitted by the dye changes based on availability of oxygen proximate to the dye; taking a fluorescence image of an area of interest within the chamber; and correlating fluorescence of the fluorescence image of the area of interest to a reference to determine an observed partial pressure of the oxygen in the area of interest.

Abstract: Metabolic engineering has developed microbial cell factories as sustainable alternatives to chemical synthesis from petroleum feedstocks or harvesting of animals and plants, but current methods can be a costly and labor-intensive commitment. Methods are described herein for microfluidic methods of screening thousands of variant cells in order to reduce time and uncertainty to provide improved strains.

Abstract: The present disclosure relates to methods for assaying and controlling micro-objects in a microfluidic device. In situ-generated hydrogel barriers are provided for dividing a microfluidic chamber into areas where assaying a cell may be performed without interference from the presence of the cell itself.

Abstract: Apparatuses and methods are described for the use of optically driven bubble, convective and displacing fluidic flow to provide motive force in microfluidic devices. Alternative motive modalities are useful to selectively dislodge and displace micro-objects, including biological cells, from a variety of locations within the enclosure of a microfluidic device.

Abstract: Methods, systems and kits are described herein for detecting the results of an assay. In particular, the methods, systems and devices of the present disclosure rely on a difference between the diffusion rates of a reporter molecule and an analyte of interest in order to quantify an amount of analyte in a microfluidic device. The analyte may be a secreted product of a biological micro-object.

Abstract: In biosciences and related fields, it can be useful to study cells in isolation so that cells having unique and desirable properties can be identified within a heterogenous mixture of cells. Processes and methods disclosed herein provide for encapsulating cells within a microfluidic device and assaying the encapsulated cells. Encapsulation can, among other benefits, facilitate analyses of cells that generate secretions of interest which would otherwise rapidly diffuse away or mix with the secretions of other cells.

Abstract: In situ-generated microfluidic isolation structures incorporating a solidified polymer network, methods of preparation and use, compositions and kits therefor are described. The ability to introduce in real time, a variety of isolating structures including pens and barriers offers improved methods of micro-object manipulation in microfluidic devices. The in situ-generated isolation structures may be permanently or temporarily installed.

Abstract: In situ-generated microfluidic isolation structures incorporating a solidified polymer network, methods of preparation and use, compositions and kits therefor are described. The ability to introduce in real time, a variety of isolating structures including pens and barriers offers improved methods of micro-object manipulation in microfluidic devices. The in situ-generated isolation structures may be permanently or temporarily installed.

Abstract: In biosciences and related fields, it can be useful to study cells in isolation so that cells having unique and desirable properties can be identified within a heterogenous mixture of cells. Processes and methods disclosed herein provide for encapsulating cells within a microfluidic device and assaying the encapsulated cells. Encapsulation can, among other benefits, facilitate analyses of cells that generate secretions of interest which would otherwise rapidly diffuse away or mix with the secretions of other cells.

Abstract: Methods of selectively positioning a micro-object in a microfluidic device are described in this application. The microfluidic device can comprise an enclosure having an inlet, an outlet, and a flow region connecting the inlet and outlet, and an electrode activation substrate having a photoconductive layer.

Abstract: In situ-generated microfluidic capture structures incorporating a solidified polymer network, methods of preparation and use, compositions and kits therefor are described. Microfluidic capture structures may be advantageously used for assays performed within the microfluidic environment, providing flexibility in assaying micro-objects such as biological cells. Assay reagents and analytes may be incorporated within the microfluidic capture structures.

Abstract: In situ-generated microfluidic capture structures incorporating a solidified polymer network, methods of preparation and use, compositions and kits therefor are described. Microfluidic capture structures may be advantageously used for assays performed within the microfluidic environment, providing flexibility in assaying micro-objects such as biological cells. Assay reagents and analytes may be incorporated within the microfluidic capture structures.

Abstract: In biosciences and related fields, it can be useful to study cells in isolation so that cells having unique and desirable properties can be identified within a heterogenous mixture of cells. Processes and methods disclosed herein provide for encapsulating cells within a microfluidic device and assaying the encapsulated cells. Encapsulation can, among other benefits, facilitate analyses of cells that generate secretions of interest which would otherwise rapidly diffuse away or mix with the secretions of other cells.

Abstract: Systems, methods, and kits therefor, enabling rapid protein evolution are described herein. A system useful in the methods described herein include a DNA synthesis component; a microfluidic system including a microfluidic device having a microfluidic channel and sequestration pens; and a computing component, which is configured to analyze assay results and, based upon the analysis, design improved DNA sequences for iterative protein evolution. The microfluidic system is configured to permit correlation of DNA sequence on a bead to its location within the microfluidic device, permit cell free protein expression of a DNA sequence captured to a bead, and to permit assay of the protein so produced.

Abstract: Methods are described herein for isolating clonal populations of cells having a defined genetic modification. The methods are performed, at least in part, in a microfluidic device comprising one or more sequestration pens. The methods include the steps of: maintaining individual cells (or precursors thereof) that have undergone a genomic editing process in corresponding sequestration pens of a microfluidic device; expanding the individual cells into respective clonal populations of cells; and detecting, in one or more cells of each clonal population, the presence of a first nucleic acid sequence that is indicative of the presence of an on-target genome edit in the clonal population of cells. Also described are methods of performing genome editing within a microfluidic device, and compositions comprising one or more clonal populations of cells generated according to the methods disclosed herein.

Abstract: Methods for screening plant cells, particularly plant protoplasts, for disease resistant traits, and kits for performing such methods are provided. The methods are performed in a microfluidic device that includes a flow region and at least one growth chamber suitable for culturing and screening a plant protoplast. The at least one surface of the growth chamber of the microfluidic chip can include a covalently linked coating material or a surface modifying ligand. The kit can comprise a microfluidic chip in combination with a reagent for detecting the viability of the plant protoplast and, optionally, a surface conditioning reagent or a surface modification reagent.

Abstract: Apparatuses and methods are described for the use of optically driven bubble, convective and displacing fluidic flow to provide motive force in microfluidic devices. Alternative motive modalities are useful to selectively dislodge and displace micro-objects, including biological cells, from a variety of locations within the enclosure of a microfluidic device.