Abstract: The present invention provides engineered cells and methods for utilizing same. Methods of enhanced carotenoid synthesis utilizing cells genetically disrupted for a yjiD, hnr or yjfP gene, or further disrupted for a gdhA, gpmB, aceE, ppc, talB or fdhF gene, or any combination thereof, or cells inhibited for their expression, activity or function are disclosed. Additionally, methods of enhanced carotenoid synthesis utilizing cells genetically disrupted for gdhA, aceE, fdhF, yjiD, hnr or yjfP gene expression or any combination thereof and ackA, appY, aspC, clp, clpP, clpXP, crcB, csdA, cyaA, evgS, fdhA, fdhD, feoB, funA, glnE, glxR, gntK, hycI, lipB, lysU, modA, moeA, nadA, nuoC, nuoK, pflB, pitA, pst, pstC, pta, p-yjiD, sohA, stpA, yagR, yaiD, ybaS, ycfZ, ydeN, yebB, yedN, yfcC, ygjP, yibD, yjfP, yjhH, or yliE gene expression, or a combination thereof or cells inhibited for their expression, activity or function are disclosed.

Abstract: Methods to create databases of peptides having a desirable property, such as antimicrobial activity, involving analyzing a database of known peptides for a pattern statistically associated with the desirable property are described herein, The set of sequences being analyzed may include sequences of a desired length containing all or substantially all combinations of amino acids that conform to at least one of the set of patterns. Once the database is identified, the database may be processed in a pattern recognition procedure that identifies a set of patterns that may be representative of a peptide having the desirable property. A set of newly generated peptides sequences may then be processed to score these new sequences against the identified patterns to correlate the patterns to the sequences and determine a degree of association or similarity between one or more of the new sequences and the set of identified patterns.

Abstract: The present invention relates generally to the use of droplets to culture and/or assay cells or other species. In some cases, the cells or other species may be sorted based upon the results of the culture and/or assay. In some embodiments, cells other species can be encapsulated in droplets and exposed to one or more agents (e.g., a sugar, an indicator dye, etc.). For instance, in some cases, exposure of cells to the agents may result in the production of metabolites or other compounds (e.g., amino acids, proteins, organic acids, etc.) which may be, for example, assayed or otherwise determined. In some embodiments, the reaction of an agent with cells and/or other species within a droplet may reveal a property of the cells or other species (e.g., sugar consumption, growth rate, ability to withstand exposure to the agent, etc.). As an example, cells that produce desired metabolites or exhibit certain properties may be separated from the other cells via sorting techniques.

Abstract: The present invention provides genetically manipulated cells and methods for utilizing same. Methods of enhanced carotenoid synthesis utilizing cells genetically disrupted for a yjiD, hnr or yjfP gene, or further disrupted for a gdhA, gpmB aceE, ppc, talB or fdhF gene, or any combination thereof, or cells inhibited for their expression, activity or function are disclosed. Methods of enhanced carotenoid synthesis utilizing cells genetically engineered to overexpress dxs, idi, yjiD, rpoS, torC, appY, ydgK, yeiA, yedR, tort, arcB, yggT, purDH, yfjN or a combination thereof, or further disrupted for the above-referenced genes are disclosed. Methods for identifying genes involved in optimized production of a carotenoid, and cells disrupted for, or inhibited for the expression, activity or function of genes thus identified are described.

Abstract: Antimicrobial peptides are small proteins used by the innate immune system to combat bacterial infection in multicellular eukaryotes. There is mounting evidence that these peptides are less susceptible to bacterial resistance than traditional antibiotics and that they may form the basis for a novel class of therapeutics. Systems and methods may treat the amino acid sequences of these peptides as a formal language and build a set of right-linear grammars that describe this language. These grammars may allow for rationally designed novel antimicrobial peptides in silico. These peptides conform to the syntax of natural antimicrobial peptides lack significant homology to any natural sequences, thus populating a previously unexplored region of protein sequence space. Synthesis of these peptides, leads to de novo AmPs.

Abstract: A structure includes a substrate and a first plurality of bilayers on the substrate. The first plurality of bilayers includes a first layer including an antimicrobial peptide having a charge, and a second layer including a polyelectrolyte having a charge opposite the charge of the first layer. At least a portion of the structure is capable of degrading by sequential removal of the first layer and the second layer, and releasing the antimicrobial peptide from the structure.

Abstract: Antimicrobial peptides are small proteins used by the innate immune system to combat bacterial infection in multicellular eukaryotes. There is mounting evidence that these peptides are less susceptible to bacterial resistance than traditional antibiotics and that they may form the basis for a novel class of therapeutics. Systems and methods may treat the amino acid sequences of these peptides as a formal language and build a set of right-linear grammars that describe this language. These grammars may allow for rationally designed novel antimicrobial peptides in silico. These peptides conform to the syntax of natural antimicrobial peptides lack significant homology to any natural sequences, thus populating a previously unexplored region of protein sequence space. Synthesis of these peptides, leads to de novo AmPs.

Abstract: The invention relates to global transcription machinery engineering to produce altered cells having improved phenotypes and methods for evaluating phenotypic diversity.

Abstract: The present invention provides cells genetically engineered to express mutated chorismate mutase/prephenate dehydrogenase (CM/PDH), the nucleic acid coding for each mutated CM/PDH and similar nucleic acids and methods for utilizing cells expressing mutated CM/PDH to produce tyrosine.

Abstract: The invention provides a device for adhering cells in a specific and predetermined position, and associated methods. The device includes a plate defining a surface and a plurality of cytophilic islands that adhere cells, isolated by cytophobic regions to which cells do not adhere, contiguous with the cytophilic islands. The islands or the regions or both may be formed of a self-assembled monolayer (SAM).

Abstract: Antimicrobial peptides enable an alternate approach to developing antimicrobial coatings due to their targeting of the membranes of the bacteria. High specific activity is achieved by orienting the peptides so that the antimicrobial ends of the peptides maximally contact the bacteria. In one embodiment, one end of the peptide is covalently attached directly to the substrate. In another embodiment, the peptides are immobilized on the substrate using a coupling agent or tether. Non-covalent methods include coating the peptide onto the substrate or physiochemically immobilizing the peptides on the substrate using highly specific interactions, such as the biotin/avidin or streptavidin system. The compositions are substantially non-leaching, antifouling, and non-hemolytic. The immobilized peptides retain sufficient flexibility and mobility to interact with and de endocytosed by the bacteria, viruses, and/or fungi upon exposure.

Abstract: A method has been developed to create databases of peptides having a desirable property, such as antimicrobial activity, based on analyzing a database of known peptides for a pattern statistically associated with an activity. One can determine a set of patterns that may be representative of a peptide having a desired characteristic or property, and evaluate a set of sequences against the set of patterns (grammars) to determine if the peptide sequence being evaluated has similar patterns to those of a peptide having the desired characteristic or property. The set of sequences being evaluated may include peptide sequences of a desired length comprising all or substantially all combinations of amino acids that conform to at least one of the set of patterns. Once the database is identified the database may be processed in a pattern recognition procedure that identifies a set of patterns that could be understood as representative of a peptide having the characteristic of interest.

Abstract: The present invention relates to expression vectors, wherein each vector comprises at least one gene of interest and a promoter operatively linked thereto wherein each promoter comprises a nucleic acid, whose sequence is randomly mutated with respect to that of the wild-type promoter and cells comprising the same. Methods utilizing either the vectors or cells of this invention, in optimizing regulation of gene expression, protein expression, or optimized gene or protein delivery are described.

Abstract: The invention relates to global transcription machinery engineering to produce altered cells having improved phenotypes.

Abstract: The present invention provides cells genetically engineered to express mutated chorismate mutase/prephenate dehydrogenase (CM/PDH), the nucleic acid coding for each mutated CM/PDH and similar nucleic acids and methods for utilizing cells expressing mutated CM/PDH to produce tyrosine.

Abstract: The present invention relates to expression cassettes libraries of expression vectors comprising the same, wherein each vector comprises at least one gene of interest and a promoter operatively linked thereto wherein each promoter comprises a nucleic acid, whose sequence is randomly mutated with respect to that of another in the library and cells comprising the same. Methods utilizing either the libraries or cells of this invention, in optimizing gene expression, protein expression, or optimized gene or protein delivery are described.

Abstract: The invention provides a device for adhering cells in a specific and predetermined position, and associated methods. The device includes a plate defining a surface and a plurality of cytophilic islands that adhere cells, isolated by cytophobic regions to which cells do not adhere, contiguous with the cytophilic islands. The islands or the regions or both may be formed of a self-assembled monolayer (SAM).

Abstract: The present invention provides genetically manipulated cells and methods for utilizing same. Methods of enhanced carotenoid synthesis utilizing cells genetically disrupted for a yjiD, hnr or yjfP gene, or further disrupted for a gdhA, gpmB aceE, ppc, talB or fdhF gene, or any combination thereof, or cells inhibited for their expression, activity or function are disclosed. Methods of enhanced carotenoid synthesis utilizing cells genetically engineered to overexpress dxs, idi, yjiD, rpoS, torC, appY, ydgK, yeiA, yedR, tort, arcB, yggT, purDH, yfjN or a combination thereof, or further disrupted for the above-referenced genes are disclosed. Methods for identifying genes involved in optimized production of a carotenoid, and cells disrupted for, or inhibited for the expression, activity or function of genes thus identified are described.

Abstract: The present invention provides engineered cells and methods for utilizing same. Methods of enhanced carotenoid synthesis utilizing cells genetically disrupted for a yjiD, hnr or yjfP gene, or further disrupted for a gdhA, gpmB, aceE, ppc, talB or fdhF gene, or any combination thereof, or cells inhibited for their expression, activity or function are disclosed. Additionally, methods of enhanced carotenoid synthesis utilizing cells genetically disrupted for gdhA, aceE, fdhF, yjiD, hnr or yjfP gene expression or any combination thereof and ackA, appY, aspC, clp, clpP, clpXP, crcB, csdA, cyaA, evgS, fdhA, fdhD, feoB, funA, glnE, glxR, gntK, hycI, lipB, lysU, modA, moeA, nadA, nuoC, nuoK, pflB, pitA, pst, pstC, pta, p-yjiD, sohA, sipA, yagR, yaiD, ybaS, ycfZ, ydeN, yebB, yedN, yfcC, ygjP, yibD, yjfP, yjhH, or yliE gene expression, or a combination thereof or cells inhibited for their expression, activity or function are disclosed.

Abstract: Antimicrobial peptides are small proteins used by the innate immune system to combat bacterial infection in multicellular eukaryotes. There is mounting evidence that these peptides are less susceptible to bacterial resistance than traditional antibiotics and that they may form the basis for a novel class of therapeutics. Systems and methods may treat the amino acid sequences of these peptides as a formal language and build a set of right-linear grammars that describe this language. These grammars may allow for rationally designed novel antimicrobial peptides in silico. These peptides conform to the syntax of natural antimicrobial peptides lack significant homology to any natural sequences, thus populating a previously unexplored region of protein sequence space. Synthesis of these peptides, leads to de novo AmPs.