Abstract: Disclosed herein are contiguous DNA sequences encoding highly compact multi-input genetic logic gates for precise in vivo cell targeting, and methods of treating disease using a combination of in vivo delivery and such contiguous DNA sequences.

Abstract: Disclosed herein are contiguous DNA sequences encoding highly compact multi-input genetic logic gates for precise in vivo cell targeting, and methods of treating disease using a combination of in vivo delivery and such contiguous DNA sequences.

Abstract: The present invention relates to a cell comprising a first nucleic acid sequence encoding a first polypeptide fused to the N-terminus of a first variant of a histidine kinase comprising a DHp domain and a CA domain, wherein said first variant does not comprise a transmembrane domain, a second nucleic acid sequence encoding a second polypeptide fused to the N-terminus of a second variant of said histidine kinase comprising a DHp domain and a CA domain, wherein said second variant does not comprise a transmembrane domain, and a third nucleic acid sequence encoding a response regulatory protein specifically phosphorylatable by said DHp domain of said first or said second variant. The present invention further relates to uses of the cell of the invention.

Abstract: The present invention relates to a method for identifying miRNA (microRNA)-modulating compounds by contacting a compound of interest with a cell comprising (i) a “miRNA-specific module” that reports specific miRNA target sequence binding by means of a first reporter product; (ii) a “non-specific RNAi module” that reports altered expression of one or more endogenous miRNAs with baseline expression levels in the cell (“non-specific miRNA markers”) by means of a second reporter product; and optionally (iii) a “gene expression module” that reports global changes in gene expression; and subsequent detection of changes in reporter product expression. The advantage of this method is that non-specific miRNA- and/or RNAi-effects of the compound of interest are detected and false positive results due to the structural similarity of different miRNAs and the commonly shared maturation pathway for most miRNAs are substantially reduced over conventional miRNA screening assays.

Abstract: The present invention is directed to a cellular biosensor system comprising (A) a repressor module comprising one or more genes, which in their cumulative gene action exert repressing and/or inhibitory effect(s) on (B), an output module comprising at least one gene comprising at least one output sequence generating one or more output signals (i) in the absence of repressing and/or inhibitory effect(s) of the repressor module (A) and (ii) in the presence of at least one recombinase expressed by (C), a recombinase module comprising at least one gene comprising at least one sequence encoding a site-specific recombinase that enables gene rearrangement in the output module resulting in one or more output signals in the absence of repressing and/or inhibitory effect(s) of the repressor module, wherein the repressing and/or inhibitory effects of the repressor module are controlled by one or more inputs that negatively affect the repressing and/or inhibitory effects of the repressor module (A).

Abstract: The invention relates to mammalian cells comprising at least one prokaryotic two-component signaling (TCS) pathway comprised of an activator protein A, a response regulator (RR) protein B activated by said protein A, such activation leading to an activated RR protein B, and an output gene C operably linked to a promoter. Transcription from said promoter is activated by activated RR protein B, and the expression of output gene C defines at least a first state (0, no transcription) and a second state (1, detectable transcription). The invention further relates to logic gates designed from such cells, and methods for integrating a plurality of output signals based on the cells and logic gates of the invention.

Abstract: The present invention relates to a method for identifying miRNA (microRNA)-modulating compounds by contacting a compound of interest with a cell comprising (i) a “miRNA-specific module” that reports specific miRNA target sequence binding by means of a first reporter product; (ii) a “non-specific RNAi module” that reports altered expression of one or more endogenous miRNAs with baseline expression levels in the cell (“non-specific miRNA markers”) by means of a second reporter product; and optionally (iii) a “gene expression module” that reports global changes in gene expression; and subsequent detection of changes in reporter product expression. The advantage of this method is that non-specific miRNA- and/or RNAi-effects of the compound of interest are detected and false positive results due to the structural similarity of different miRNAs and the commonly shared maturation pathway for most miRNAs are substantially reduced over conventional miRNA screening assays.

Abstract: The invention relates to mammalian cells comprising at least one prokaryotic two-component signaling (TCS) pathway comprised of an activator protein A, a response regulator (RR) protein B activated by said protein A, such activation leading to an activated RR protein B, and an output gene C operably linked to a promoter. Transcription from said promoter is activated by activated RR protein B, and the expression of output gene C defines at least a first state (0, no transcription) and a second state (1, detectable transcription). The invention further relates to logic gates designed from such cells, and methods for integrating a plurality of output signals based on the cells and logic gates of the invention.

Abstract: The present invention is directed to a cellular biosensor system comprising (A) a repressor module comprising one or more genes, which in their cumulative gene action exert repressing and/or inhibitory effect(s) on (B), an output module comprising at least one gene comprising at least one output sequence generating one or more output signals (i) in the absence of repressing and/or inhibitory effect(s) of the repressor module (A) and (ii) in the presence of at least one recombinase expressed by (C), a recombinase module comprising at least one gene comprising at least one sequence encoding a site-specific recombinase that enables gene rearrangement in the output module resulting in one or more output signals in the absence of repressing and/or inhibitory effect(s) of the repressor module, wherein the repressing and/or inhibitory effects of the repressor module are controlled by one or more inputs that negatively affect the repressing and/or inhibitory effects of the repressor module (A).

Abstract: Provided herein are high-input detector modules and multi-input biological classifier circuits and systems that integrate sophisticated sensing, information processing, and actuation in living cells and permit new directions in basic biology, biotechnology and medicine. The multi-input biological classifier circuits described herein comprise synthetic, scaleable transcriptional/post-transcriptional regulatory circuits that are designed to interrogate the status of a cell by simultaneously sensing expression levels of multiple endogenous inputs, such as microRNAs. The classifier circuits then compute whether to trigger a desired output or response if the expression levels match a pre-determined profile of interest.

Abstract: Provided herein are high-input detector modules and multi-input biological classifier circuits and systems that integrate sophisticated sensing, information processing, and actuation in living cells and permit new directions in basic biology, biotechnology and medicine. The multi-input biological classifier circuits described herein comprise synthetic, scaleable transcriptional/post-transcriptional regulatory circuits that are designed to interrogate the status of a cell by simultaneously sensing expression levels of multiple endogenous inputs, such as microRNAs. The classifier circuits then compute whether to trigger a desired output or response if the expression levels match a pre-determined profile of interest.

Abstract: A device, system and method for molecular computing which not only includes a suitable, renewable power source, but actually is able to receive power through the performance of the computations themselves. The molecular computing machine of the present invention actually employs the free-energy difference between its input and output to accomplish a computation, preferably by using its input DNA molecule as a partial source of energy, or alternatively by using the input DNA molecule as the sole source of energy. This molecular finite automaton preferably transforms an input DNA molecule into an output DNA molecule by digesting the input as it computes.

Abstract: Disclosed herein are autonomous molecular circuits that can function in cells. The circuits can process logical operations in which one or more input cues are among the operands and produce an appropriate output. Such circuits can be implemented in living cells, e.g., eukaryotic or prokaryotic cells that have been modified to include circuit components. The molecular circuits and cells containing the circuits can be used in a variety of applications including, e.g., diagnostics, therapeutics, and protein production.

Abstract: An autonomous molecular computer that, when coupled to a molecular model of a disease, is capable of disease diagnosis. The computer preferably performs such diagnosis by detecting one or more disease markers. For example, optionally and preferably the molecular computer checks for the presence of over-expressed, under-expressed and mutated genes, applies programmed medical knowledge to this information to reach a diagnostic decision.

Abstract: A device, system and method for molecular computing which not only includes a suitable, renewable power source, but actually is able to receive power through the performance of the computations themselves. The molecular computing machine of the present invention actually employs the free-energy difference between its input and output to accomplish a computation, preferably by using its input DNA molecule as a partial source of energy, or alternatively by using the input DNA molecule as the sole source of energy. This molecular finite automaton preferably transforms an input DNA molecule into an output DNA molecule by digesting the input as it computes.