Abstract: Compositions and methods for identifying and using cis-regulatory and decoy sequences.

Abstract: This invention is directed to applying a low sedimental fluid shear environment to manipulate microorganisms, and to microorganisms and compositions obtained based on such manipulation. Specifically, the present invention provides methods of modifying a molecular genetic or phenotypic characteristic (e.g., virulence, stress resistance or biofilm formation) of a microorganism by culturing in a low sedimental shear environment. One or more ion concentrations in the culture can be modulated in order to inhibit or amplify the extent of the modification. The present invention also provides microorganisms obtained from a low sedimental shear culture, which exhibit modified and desirable phenotypic characteristics, as well as therapeutic, vaccine and bioindustrial products prepared from such microorganisms.

Abstract: The present invention relates to a polymyxin derivative wherein R1, R2 and R3 are optional and R1, R2, R3, R5, R8 and R9 are cationic or neutral amino acid residues selected so that the total number of positive charges at physiological pH is at least two but no more than three; and to a combination product comprising at least two such derivatives.

Abstract: The present invention relates to the use of compounds of the general Formula (I): wherein in Formula (I), R is H, alkyl, cycloalkyl, aryl or heteroaryl; R1 is H, alkyl, cycloalkyl, aryl or heteroaryl; R2 is H, alkyl, cycloalkyl, aryl or heteroaryl; A1 and A2 each independently represent an optionally substituted C1-C20-alkyl group which may contain one or more group(s) Z, or a monocyclic or polycyclic optionally substituted aromatic or non-aromatic ring system which may contain one or more group(s) X, and in case of a polycyclic ring system, said system contains at least one aromatic ring; Z is selected from the group consisting of S, O, N, NR4, CO, CO2, CS, SO or SO2 X is selected from the group consisting of S, O, N, NR4, SO or SO2;

Abstract: Disclosed herein are cyanide-tolerant nitrile hydratases especially from Pseudomonas putida or Pseudomonas marginalis strains which exhibit increased cyanide tolerance. Also disclosed are methods of preparing amides from nitriles in the presence of cyanides and polynucleotide sequences coding for cyanide-tolerant nitrile hydratases.

Abstract: The present invention provides compositions and methods for modulating bacterial quorum sensing using antagonist or agonist compounds. Further, the present invention provides methods of treating or preventing microbial damages and diseases, in particular for diseases where there is an advantage in inhibiting quorum sensing regulated phenotypes of pathogens.

Abstract: The present disclosure relates to isolation, identification and application of Shewanella putrefaciens strain LH4:18 that grows, under denitrifying anaerobic conditions, on crude oil as the sole carbon source. This organism assists in oil release from substrate in reservoir simulations when grown on either lactate or peptone as a carbon source. Shewanella putrefaciens strain LH4:18 can be used alone or in concert with other microorganisms to improve oil recovery.

Abstract: The present invention relates to improved methods for the production, isolation and purification of epothilone B. These methods include, for example, a fermentation process for the production of epothilone B, isolation via adsorption onto a resin, and subsequent purification.

Abstract: The present invention relates to a method for producing L-methionine and organic acid comprising the following steps: Step 1) preparing a strain producing L-methionine precursor and producing L-methionine precursor by the fermentation of the strain; Step 2) producing L-methionine and organic acid by the enzyme reaction process with the L-methionine precursor as a substrate, and microorganism strains used in each step.

Abstract: A process for producing a sulfur-containing ?-hydroxycarboxylic acid compound, which comprises a step for reacting a sulfur-containing dihydroxy compound with a cell or a material from treated cell of a microorganism that has an ability to convert the sulfur-containing dihydroxy compound to a corresponding ?-hydroxycarboxylic acid compound.

Abstract: This invention relates to a process for producing an amide compound from a nitrile compound using a microbial catalyst, wherein a microbial cell having nitrile hydratase activity of 50 U or higher per mg of dry cell at a reaction temperature of 10° C. is brought into contact with a nitrile compound in an aqueous medium without being immobilized. This method utilizes a microbial cell that exhibits high nitrile hydratase activity in the reaction without being entrap-immobilized. Thus, an amide compound can be effectively produced from a nitrile compound without problems of decreased reaction speed or lowered amount produced per unit cell amount, which are caused by entrap-immobilization. Accordingly, an amide compound can be produced within a very short period of time in the case of a batch reaction and with a very small-scale facility in the case of a continuous reaction.

Abstract: This invention relates to a process for the production of organic formulation of bio pesticide containing Pseudomonas Fluorescens comprising preparation of Mother culture of P. fluorescens and inoculating in King's B broth, at 30±1° C. for 24-36 hours followed by liquid fermentation process in 5-10% pongamia cake aqueous extract, 5-10% neem cake aqueous extract, 0.3-0.5% sugarcane molasses and King's B broth followed by solid fermentation using sterile Pongamia deoiled cake, Neem deoiled cake, wheat Bran.

Abstract: The present invention relates to an environment friendly, safe, and efficient four-step method of bio-bleaching Kraft pulp using the following strains of bacteria: (a) Serratia marcescens, MTCC 5094, (b) Pseudomonas aeruginosa, MTCC 5095, (c) Providencia rettgeri, MTCC 5096, (d) Pseudomonas aeruginosa, MTCC 5098. The present invention also provides a microbial consortium comprising a synergistic mixture of ligninolytic bacterial isolates Serratia marcescens, MTCC 5094, Pseudomonas aeruginosa, MTCC 5095, and Pseudomonas aeruginosa, MTCC 5098, or comprising bacterial strains Providencia rettgeri, MTCC 5096, Serratia marcescens, MTCC 5094, Pseudomonas aeruginosa, MTCC 5095, and Pseudomonas aeruginosa, MTCC 5098, and a process for preparing an inoculum of the bacterial isolate Providencia rettgeri, MTCC 5096.

Abstract: The present invention relates to the production of secondary metabolites from microorganisms. In particular, there are provided methods for inducing the rapid production of such compounds from a variety of microorganisms.

Abstract: Bacteria that are not natural butanol producers were found to have increased tolerance to butanol when the membrane content of unsaturated trans fatty acids was increased. Feeding cells with unsaturated trans fatty acids increased their concentration in the membrane, which may also be accomplished by expressing a fatty acid cistrans isomerase.

Abstract: Embodiments of the present invention relates to the incorporation and use of a regulated genetic suicide mechanism for use in the improved purification of biologics, including adjunct use in various eubacterial minicell production and purification methodologies. Described herein are high-yield eubacterial minicell-producing strains with genetic modifications that comprise a regulated genetic suicide mechanism that irreparably destroys the parent cell chromosome such that live parental cells in a culture can be functionally eliminated at any time during the course of a minicell production and purification run. Embodiments of the present invention also describe methods useful in the elimination of live parental cells during the production of other cell-based biologics.

Abstract: According to the present invention a new isolate of a Pseudomonas spp, DSM 21663, has been shown to possess unique properties. This Pseudomonas is a plant growth-promoting rhizobacterium (PGPR). Among its modes of action involved in plant growth-promotion are anti-biotic production (2,4-diacetylphloroglucinol, (DAPG); pyrrolnitrin, PRN and others), indole-3-acetic acid (IAA) production and phosphate solubilization, and production of unique volatiles. The strain is fluorescent, oxidase-positive, and has the ability to suppress soil-borne root and foliar pathogens of both fungal and bacterial origin.

Abstract: A metalloprotease that converts TNF-? from the 26 kD cell form to the 17 kD form has been isolated and purified and the cDNA sequence known. In particular, the protease has a molecular weight of approximately 80 kD. The isolated and purified protease is useful for designing an inhibitor thereof, and may find use as a therapeutic agent. Assays for detecting the protease-inhibiting activity of a molecule are also an aspect of the invention.

Abstract: The present invention relates to methods of detecting and regulating cellular DNA damage as well as methods of screening compounds suitable for modulating cellular DNA damage. The methods of the present invention utilize antibodies that selectively bind to a phosphorylated tyrosine residue in a SQEY tyrosine phosphorylation motif sequence or a phosphorylated serine residue in a KENSSQ phosphorylation motif sequence, where the phosphorylated serine residue is closest to the glutamine residue. Also encompassed by the present invention are methods of treating a subject having cancer. These methods involve the administration of an agent that modulates the phosphorylation of the tyrosine residue in a SQEY motif. Suitable agents for modulating the phosphorylation of the tyrosine residue of the SQEY motif are also disclosed.

Abstract: Biotinylation of compounds such as peptides and peptidomimetics facilitates illicit transport of the compounds into Gram negative bacteria.

Abstract: Problem to be Solved: To provide a new microorganism capable of producing a polyhydroxyalkanoate (PHA), a PHA synthase gene, an expression cassette including the gene, a vector including the expression cassette, a transformant transformed by the vector, a polypeptide having PHA synthase activity, a method for producing a PHA synthase and a method for producing a PHA. Solution: The new microorganism is capable of producing a polyhydroxyalkanoate comprising a 16S rRNA gene whose polynucleotide sequence shows 99% or more homology to a polynucleotide sequence represented by SEQ ID No: 1, having an optimum temperature of an activity temperature range for the growth and PHA production of the microorganism of at least 45° C. and being capable of growing at a pH range from 6 to 10.

Abstract: The present invention provides microorganisms, in which the activity of 4-hydroxybenzoate polyprenyltransferase or 2-octaprenylphenol?2-octaprenyl-6-methoxyphenol flavin reductase is reduced or lost, and which have an ability to produce lactic acid, in particular, microorganisms comprising a chromosomal DNA in which a gene encoding a protein having 4-hydroxybenzoate polyprenyltransferase activity or a protein having 2-octaprenylphenol?2-octaprenyl-6-methoxyphenol flavin reductase activity is partially or completely defective; and a process for producing lactic acid using the microorganisms.

Abstract: A device and method for growing aerobic and facultatively anaerobic bacteria such as Pseudomonas Fluorescens, Bacillus subtilus, Bacillus lichenoformis, Starkeya novella and various autotrophic sulfur metabolizing bacteria, along with methods for releasing these bacteria into suspended growth or fixed film wastewater treatment zones such as soil or media, for the purposes of bioremediation and the removal of nitrogen, sulfur, and carbon wastes.

Abstract: The object of the present invention is to provide a microorganism which places little burden on the environment, shows an extremely low possibility of a resistant pathogenic bacterium to emerge, and has a superior controlling ability against various plant diseases (in particular, soft rot and canker of leaf and root vegetables); a plant disease controlling agent containing the microorganism; and a method for controlling plant diseases comprising applying the plant disease controlling agent to the plant and/or the grove soil thereof. A plant disease controlling agent is used which contains a bacterial cell of Pseudomonas rhodesiae having controlling ability against plant diseases, preferably a bacterial cell of Pseudomonas rhodesiae FERM BP-10912 or its variant having controlling ability against plant diseases.

Abstract: The invention provides a novel system for the tunable expression of nucleic acids encoding e.g., polypeptides such as recombinant proteins in prokaryotic systems. The system is based on the ability of T7 lysozyme (T7Lys) to inhibit the activity of T7RNAP. Expression of T7Lys can be continuously adjusted as its expression is under the control of a promoter whose activity can be titrated. The invention provides a host cell capable of expressing T7 RNA polymerase, the host cell comprising a first nucleic acid having a T7 lysozyme gene or a T7 lysozyme variant gene and a tunable promoter for controlling the expression of the T7 lysozyme gene. It also provides a host cell further comprising a second nucleic acid having a T7 promoter operably linked to a nucleic acid sequence encoding a target polypeptide, whereby expression of the target polypeptide is tuned via controlling the expression of the T7 lysozyme gene.

Abstract: The present disclosure relates to isolation and identification of unique Pseudomonas stutzeri strains that can grow on crude oil under denitrifying conditions and are useful in oil recovery.

Abstract: The present invention relates to compositions and methods for reducing or inhibiting biofilm comprising modulating expression of a cysB gene in a cell. The invention also provides methods for modulating the expression of a cysB, cysD, cysI, cysJ, cysK, and ybiK. The invention further provides methods for identifying gene(s) involved in biofilm formation and for identifying biofilm inhibitors.

Abstract: Disclosed are compositions comprising variants of alpha-amylase that have alpha-amylase activity and which exhibit altered properties relative to a parent AmyS-like alpha-amylase from which they are derived. The compositions comprise an additional enzyme such as a phytase. Also disclosed are methods of using the compositions, and kits related thereto.

Abstract: The present invention relates to compositions comprising CpG rich DNA from Pseudomonas aeruginosa. The compositions optionally comprise a cupredoxin. The present invention includes specific CpG DNAs from Pseudomonas aeruginosa that are useful for treating cancer and other conditions in patients. These compositions are optionally in a pharmaceutically acceptable carrier and also optionally comprise a cupredoxin. The present invention further relates to methods to express proteins near cancer cells. These methods may be used to express therapeutic or diagnostic proteins near cancer cells in a patient suffering from cancer or other conditions, and can also be used for diagnosing cancer in a patient. This method uses the gene for azurin from P. aeruginosa as an expression system for azurin or heterologous proteins in P. aeruginosa or heterologous cells.

Abstract: The invention relates to an non-pathogenic and/or attenuated bacterium which is capable of inducing apoptosis in macrophages.

Abstract: Provided are a novel microorganism and a method for purifying 2,6-naphthalene dicarboxylic acid with high purity using the microorganism. The microorganism is Pseudomonas sp. Strain HN-72 isolated from soil and has the ability to convert 2-formyl-6-naphthoic acid contained as an impurity in a crude naphthalene dicarboxylic acid, which is an oxidation product of 2,6-dimethylnaphthalene, to 2,6-naphthalene dicarboxylic acid. The Pseudomonas sp. strain HN-72 has excellent effects in producing high-purity 2,6-naphthalene dicarboxylic acid in high yield.

Abstract: The present invention relates to a bacterium strain of accession no. MTCC 5099, a process for the preparation of inoculum of the said strain, and a process for the reduction of color from pulp mill effluent using the above said inoculum, which comprises steps of inoculating appropriate aliquots of the pulp and paper mill effluent with the cell slurry obtained, incubating the mixture at about 37 degree C. at about 100 rpm for time duration ranging between 24-48 hours, assessing color and total lignin levels to determine the color removal efficiency of the above said bacterium.

Abstract: A method for producing one or more pseudomycins is described including cultures of Pseudomonas syringae that produce one or more pseudomycins having general formula (I) where R is a lipophilic moiety.

Abstract: This invention provides a novel bacterial sialic acid transporter that is a member of the family of ABC transporters. The transporter is a useful target for pharmaceuticals.

Abstract: A method for cleavage of the ether-linkage of polyethoxylates is described. A novel pure microbial culture, Pseudomonas nitroreducens TX1 (Depository No.: BCRC910228), is used under aerobic condition to cleave the ether-linkage adjacent to the carboxylated terminus or ethoxyl terminus. This method is useful to cleave sequentially ether-linkage of polyethoxylates in an aqueous buffer solution with an initial concentration of the polyethoxylates between 0.05% and 20%. This method is also effective for the cleavage of the ether-linkages in short-chain polyethoxylates with one to three ethoxyl units.

Abstract: There is a biological composition and method of use for generating and feeding microorganisms that are intended for distribution in an agricultural system. Included is a micro-organism quantity, and a nutrient quantity which may have a supplement, a short-term nutrient and a long term nutrient. The composition may be applied to a container having water wherein the microorganisms rapidly reproduce. As the microorganisms reproduce they may be extracted. Once extracted, they may be introduced into an ecosystem, such as being injected into an irrigation system and being dispersed over crops and crop soil. There, the microorganisms may enhance vegetation growth, health, production, strength and efficiency by producing cellulase enzymes, converting nutrients to a form usable by vegetation, loosening soil, enhancing water retention in soil, and/or combating parasitic organisms.

Abstract: The present invention relates to an antibacterial agent containing 7,10-dihydroxy-8(E)-octadecenoic acid (referred as DOD) as an active ingredient. DOD produced by the method of the present invention can be effectively used as an antibacterial agent because it has a wide spectrum of antibacterial activity against various microorganisms.

Abstract: The present invention provides a new supply source of phospholipase A1, which is useful for phospholipid modification and lipid biochemical research, and offers a method capable of efficiently manufacturing a large amount of high DHA content phospholipids and lysophospholipids. A novel microorganism HFKI-0020 (FERM AP-20545) of the genus Pseudomonas which produces enzymes with phospholipase A1 activity can be used as a new supply source of enzymes with the phospholipase A1 activity. A lipid-modifying agent containing an effective dose of enzymes with the phospholipase A1 activity produced by those novel microorganisms allows the efficient mass-production of lysophospholipids.

Abstract: The present invention provides a bacterial strain which is able to degrade or mineralize s-triazine compounds, such as simazine, which corresponds to Pseudomonas sp. strain MHP41, deposited under the accession number NRRL B-30908. The present invention provides a product for the bioremediation of environments contaminated with s-triazine, where the product includes a bacterial inoculum of Pseudomonas sp. strain MHP41. The present invention further provides a method for the bioremediation of environments contaminated with s-triazines, which uses this product for the bioremediation.

Abstract: Novel strains of isolated and purified bacteria have been identified which have the ability to degrade petroleum hydrocarbons including a variety of PAHs. Several isolates also exhibit the ability to produce a biosurfactant. The combination of the biosurfactant-producing ability along with the ability to degrade PAHs enhances the efficiency with which PAHs may be degraded. Additionally, the biosurfactant also provides an additional ability to bind heavy metal ions for removal from a soil or aquatic environment.

Abstract: This invention relates to amylase polypeptides, and nucleic acids encoding the polypeptides and uses thereof. The amylases of the present invention have been engineered to have more beneficial qualities. Specifically the amylases of the current invention show an altered exospecifity.

Abstract: The invention provides a non-naturally occurring microorganism having one or more gene disruptions, the one or more gene disruptions occurring in genes encoding an enzyme obligatory coupling 3-hydroxypropionic acid production to growth of the microorganism when the gene disruption reduces an activity of the enzyme, whereby the one or more gene disruptions confers stable growth-coupled production of 3-hydroxypropionic acid onto the non-naturally occurring microorganism.

Abstract: A Gram-negative bacterial strain, Pseudomonas putida TX2 (PTA-6169 and BCRC 910232), was isolated from farmland, which had received frequent applications of a various pesticides and surfactants. This strain was demonstrated to have the capacity to grow on alkylphenol polyethoxylates (0.05% to 20%) or alkylphenol (0.001% to 0.01%) as sole source of carbon and energy. The metabolic activity of this strain can be applied in the degradation of organic polymers containing ethoxylate units, alkylphenol and alkylphenol derivatives.

Abstract: This invention provides identification and characterization of racemases and epimerases and definition of protein signatures of those racemases and epimerases. This invention also provides identification of nucleic acid molecules encoding a peptide consisting of a motif characteristic of the protein signatures, and to the peptides consisting of these motifs. Antibodies specific for the peptides and to immune complexes of these antibodies with the peptides are also provided. Further, the invention relates to methods and kits for detecting racemases and epimerases using the nucleic acid molecules of the invention, as well as the peptides consisting of the motifs and antibodies to these peptides.

Abstract: The present invention provides a microorganism which comprises a chromosomal DNA lacking a part or entire of the gene encoding a protein having the amino acid sequence as shown in SEQ ID NO: 1 or 2, or the gene encoding a protein having 80% or more homology with the amino acid sequence as shown in SEQ ID NO: 1 or 2, and has the ability to produce a useful substance; a process for producing a useful substance using said strain; especially a process for producing a useful substance which is selected from the group consisting of proteins, peptides, amino acids, nucleic acids, vitamins, saccharides, organic acids, and lipids.

Abstract: A reporter system reflecting the transport process that transports GPI-anchored proteins to the cell wall was constructed and compounds inhibiting this process were discovered. Further, fungal genes conferring resistance to the above compounds were identified and methods of screening for compounds that inhibit the activity of the proteins encoded by these genes were developed. These genes encode proteins participating in fungal cell wall synthesis. Therefore, through the novel compounds, the present invention showed that antifungal agents having a novel mechanism, i.e. inhibiting the process that transports GPI-anchored proteins to the cell wall, could be achieved.

Abstract: The invention relates to a process for the biocatalytic oxidation of aromatic compounds using recombinant xylene monooxygenase-expressing microorganisms in a biphasic reaction medium.

Abstract: A process for biological production of ortho-aminophenols from nitroaromatic compounds using recombinant E. Coli strains. The process uses an enzyme system that makes use of a nitroreductase enzyme that initially reduces the nitroarene to the hydroxylaminoarene and a mutase enzyme that converts the hydroxylaminoarene to an ortho-aminophenol.

Abstract: The present invention provides a method of treatment to improve wound healing and to minimize/prevent abnormal scarring caused by tissue contraction and fibrosis formation by providing a specific gene, Wit 3.0 alpha and beta sequences that is differentially expressed in wounded oral mucosa cells, relative to their decreased expression in non-wounded oral mucosa cells. One aspect of the invention is a method to treat soft tissue wound using anti-sense nucleic acid technologies. Another aspect of the present invention is a method to treat soft tissue wound using sense nucleic acid technologies. These methods can employ a complimentary nucleic acid sequence that is greater than 85% identity to Wit 3.0 alpha and/or beta sequences or greater than 90% identity to the deduced amino acids thereof.

Abstract: Plants and crops subject to attack by fungal related diseases are protected or treated by the application of Pseudomycin compositions which were originally isolated from Pseudomonas syringae.