University of California

Taxon Biosciences Inc.

Other

Rosetta Inpharmatics, Inc.

Taxon Biosciences in (pioneer Pat)

Matthew N Ashby

Jasper D Rine

Ladonna Wood

Ulrika Lidstrom

Matthew Cornyn Kuchta

Victor Kunin

Caroline Kostecki

Christopher P Belnap

Natalia Shestakova

Christine M Clarke

Bradley James Huizinga

Dariusz Strapoc

Adewale J Lambo

Alison Gould

Victor L Boyartchuk

Daniel D Shoemaker

Stewart Scherer

Michael Ziman

John W Phillips

Nicholas Marini

Ulrika Lidström

The present application relates to plant growth promoting microbes (PGPMs), compositions comprising these PGPMs and methods of using these PGPMs and/or compositions for enhancing plant health, plant growth and/or plant yield, and/or for preventing, inhibiting, or treating the development of plant pathogens or the development of phytopathogenic diseases. This application also provides non-naturally occurring plant varieties that are artificially infected with a PGPM descried herein, as well as seed, reproductive tissue, vegetative tissue, regenerative tissues, plant parts, or progeny thereof.

Plant growth-promoting microbes, compositions, and uses

This invention generally relates to natural gas and methylotrophic energy generation, bio-generated fuels and microbiology. In alternative embodiments, the invention provides nutrient amendments and microbial compositions, e.g., consortia, that are both specifically optimized to stimulate methanogenesis, or for 'methylotrophic' or other conversions. In alternative embodiments, the invention provides methods to develop nutrient amendments and microbial compositions that are both specifically optimized to stimulate methanogenesis in a given reservoir. The invention also provides methods for the evaluation of potentially damaging biomass formation and scale precipitation resulting from the addition of nutrient amendments. In other embodiments, the invention provides methods for simulating biogas in sub-surface conditions using a computational model.

Compositions and methods for identifying and modifying carbonaceous compositions

The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

Databases for rRNA gene profiling of microbial communities

DNA-based methods of geochemical prospecting

The present invention relates to methods of identifying genes whose expression is indicative of activation of a particular biochemical or metabolic pathway or a common set of biological reactions or functions in a cell ('regulon indicator genes') The present invention provides an example of such an indicator gene. The present invention also relates to methods of partially characterizing a gene of unknown function by determining which biological pathways, reactions or functions its expression is associated with, thereby placing the gene within a functional genetic group or 'regulon'. These partially characterized genes may be used to identify desirable therapeutic targets of biological pathways of interest (&#x201c;regulon target genes&#x201d;) The present invention provides examples of such target genes. Methods for identifying effectors (activators and inhibitors) of regulon target genes are provided. The present invention also provides examples of regulon target gene inhibitors.

Methods for the identification of inhibitors of an isoprenoid metabolic pathway

Two genes which encode polypeptides that mediate post-prenylation processing steps in CAAX polypeptides such as Ras are provided. The two genes (AFC1 and RCE1) encode polypeptides that mediate the removal of the AAX tripeptide from the CAAX polypeptide following prenylation. The genes and encoded polypeptides provide assays for testing compounds for an effect on post-prenylation processing steps. A heat shock assay for assessing Ras activity is also provided.

AFC1 and RCE1: isoprenylated CAAX processing enzymes

Methods for the survey and genetic analysis of populations

Stimulus-response patterns are analyzed using deduction protocols applied through AI systems such as expert systems and neural networks. Generating an output signal matrix database involves: (i) constructing a stimulated physical matrix; (ii) detecting a physical signal at each unit of the physical matrix; (iii) transducing each physical signal to generate an electrical output signal; (iv) storing each output signal in an output signal matrix data structure; and (v) repeating steps (i)-(iv) to iteratively store output signal matrix data structures for a plurality of stimuli to form an output signal matrix database. Individual output signal matrices are compared to such output signal matrix databases according for qualitative analysis. The stimulated physical matrices comprise an ordered array of units, each confining (1) either a different responder of a living thing or a probe corresponding to such a different responder and, (2) an identifier for the responder or probe. The living thing is provided a stimulus capable of repressing the responders of a plurality of the units and the identifier provides a physical signal corresponding to the repression of such different responder.

Systems for generating and analyzing stimulus-response output signal matrices

The present invention provides methods of screening for a molecule that inhibits the expression or activity of a protein encoded by a target gene which affects the fitness of a cell. The methods are based on a co-culture assay, and entail culturing together two cell populations, each of which is a population of identical cells, of the same species that differs substantially only in the expression or activity of the gene to be targeted or its encoded protein and the presence or absence of a reporter gene. The screen can be applied to cultured cells, unicellular and multicellular organisms. Manipulating the expression or activity of the target gene sensitizes the host to a molecule which inhibits the target gene or its encoded protein such that the cell or organism comprising the manipulated target gene grows at a different rate from the cell or organism comprising the unmanipulated gene in response to exposure to the molecule. The methods of the invention can be used for identifying drugs, proteins or any other molecules that inhibit the function of proteins encoded by target genes.

Targeted methods of drug screening using co-culture methods

Systems for generating and analyzing stimulus-response output signal

Methods and compositions for modeling the transcriptional responsiveness of an organism to a candidate drug involve (a) detecting reporter gene product signals from each of a plurality of different, separately isolated cells of a target organism, wherein each cell contains a recombinant construct comprising a reporter gene operatively linked to a different endogenous transcriptional regulatory element of the target organism such that the transcriptional regulatory element regulates the expression of the reporter gene, and the sum of the cells comprises an ensemble of the transcriptional regulatory elements of the organism sufficient to model the transcriptional responsiveness of said organism to a drug; (b) contacting each cell with a candidate drug; (c) detecting reporter gene product signals from each cell; (d) comparing reporter gene product signals from each cell before and after contacting the cell with the candidate drug to obtain a drug response profile which provides a model of the transcriptional responsiveness of said organism to the candidate drug.

Methods for drug screening

Growing community of inventors

Mill Valley, CA, United States of America

Matthew N Ashby