Eric S Davidson

US Patent:

7720614, May 18, 2010

Filed:

Dec 7, 2005

Appl. No.:

11/297293

Inventors:

Eric H. Davidson - Pasadena CA, US
Robert Andrew Cameron - Pasadena CA, US

Assignee:

California Institute of Technology - Pasadena CA

International Classification:

G01N 33/48

US Classification:

702 20, 703 2, 703 11, 706 45, 707 6, 707 7, 435 6, 4353201, 536 242, 211 4112

Abstract:

A computational method is described which uses the process of cis-regulatory module evolution to identify conserved sequence patches which exhibit suppression of change by snp/indel occurrence, including determining sequence similarities significantly greater than random expectation on selected genome sequences from two or more species in sequences that lie outside of protein coding regions, sorting the similarities for conserved patches of single nucleotide polymorphisms (SNPs) and insertion/deletions (indels). and selecting such patches to identify cis-regulatory modules. Further, the disclosed method is practiced in the absence of having to execute multiple interspecific sequence comparison analysis, where such identified cis-regulatory modules are used to produce libraries and arrays containing such cis-regulatory modules.

US Patent:

8178347, May 15, 2012

Filed:

Aug 20, 2007

Appl. No.:

11/894804

Inventors:

Eric H. Davidson - Pasadena CA, US

Assignee:

California Institute of Technology - Pasadena CA

International Classification:

C12N 5/00
C12N 5/02
C07H 21/02

US Classification:

435325, 536 231

Abstract:

The invention provides a method of modulating a regulatory state of a cell. The method consists of: (a) identifying a point of interdiction within a cis regulatory network specifying a genetic regulatory architecture of a cell, and (b) introducing into a progenitor cell two or more network elements within said network to induce a predetermined series of cis regulatory network interactions resulting in a specified regulatory state of said progenitor cell. Also provided is a method of modulating a regulatory state of a cell. The method consists of: (a) identifying a point of interdiction within a cis regulatory network specifying a genetic regulatory architecture of a cellular state, and (b) introducing into a progenitor cell two or more network elements within said network to induce a predetermined series of cis regulatory network interactions resulting in a specified regulatory state of said progenitor cell. A cell having a specified regulatory state consisting of a modified genetic regulatory architecture is further provided. Methods of diagnosing and methods of treating an individual suffering from a cellular defect also are provided.

US Patent:

20040033601, Feb 19, 2004

Filed:

May 30, 2003

Appl. No.:

10/452766

Inventors:

Eric Davidson - Pasadena CA, US

International Classification:

C12N015/85

US Classification:

435/455000

Abstract:

The invention provides a method of modulating a regulatory state of a cell. The method consists of: (a) identifying a point of interdiction within a cis regulatory network specifying a genetic regulatory architecture of a cell, and (b) introducing into a progenitor cell two or more network elements within said network to induce a predetermined series of cis regulatory network interactions resulting in a specified regulatory state of said progenitor cell. Also provided is a method of modulating a regulatory state of a cell. The method consists of: (a) identifying a point of interdiction within a cis regulatory network specifying a genetic regulatory architecture of a cellular state, and (b) introducing into a progenitor cell two or more network elements within said network to induce a predetermined series of cis regulatory network interactions resulting in a specified regulatory state of said progenitor cell. A cell having a specified regulatory state consisting of a modified genetic regulatory architecture is further provided. Methods of diagnosing and methods of treating an individual suffering from a cellular defect also are provided. The invention additionally provides a method of identifying a compound having differentiation or cell fate inducing activity.

US Patent:

20070113295, May 17, 2007

Filed:

Sep 25, 2006

Appl. No.:

11/526303

Inventors:

Eric Davidson - Pasadena CA, US
Joel Smith - Lacanada CA, US

Assignee:

California Institute of Technology - Pasadena CA

International Classification:

A01K 67/027
C12N 5/06

US Classification:

800008000, 800014000, 435455000, 435325000

Abstract:

The invention relates to methods of regulating gene expression, e.g., to turn on or off, or up or down gene expression in an organism when and where desired, without the toxic side effects usually associated with other contemporary methods, such as those toxic side effects caused by introducing compounds that do not naturally occur in life.

US Patent:

57834202, Jul 21, 1998

Filed:

Aug 27, 1997

Appl. No.:

8/919002

Inventors:

Eric H. Davidson - Pasadena CA

Assignee:

California Institute of Technology - Pasadena CA

International Classification:

C12P 2102
C12N 1563
C12N 1513

US Classification:

435 691

Abstract:

The present invention is directed to methods and compositions useful for altering the transcriptional expression of genes in eukaryotic cells. The invention employs novel antibody derivative molecules which function to recognize and bind to specific cis-regulatory DNA sequence elements of a eukaryotic gene. When two antibody derivative molecules are bound to adjacent cis-regulatory DNA sequence elements of a gene, those molecules may interact to form an antibody binding site which is capable of recognizing and binding to a transcription factor protein for the target gene, thereby affecting the functionality of that transcription factor protein and, in turn, the transcriptional activity of the gene. Also provided herein are isolated nucleic acids encoding the novel antibody derivative molecules of the present invention and expression vectors comprising those nucleic acids.

US Patent:

45915679, May 27, 1986

Filed:

Aug 8, 1983

Appl. No.:

6/520756

Inventors:

Roy J. Britten - Costa Mesa CA
Eric H. Davidson - Pasadena CA

Assignee:

California Institute of Technology - Pasadena CA

International Classification:

C12M 132
C12M 126
C12Q 168
C12Q 124

US Classification:

435293

Abstract:

A system for the production and maintenance of genomic libraries of recombinant DNA in a fixed geometric array arranged so that such libraries may be accurately replicated and maintained with the same set of individual DNA inserts occupying reproducible locations and comprising, (a) sets of individual bacterial colonies or plaques of bacteriophage which contain inserts of animal or plant DNA and are present in so large a number that there will be a high probability that the complete library will contain each DNA sequence of all of the sequences present in an animal or plant genome; to be established in subarrays which can individually be replicated, (b) a subsystem for picking up inocula from each of a geometric array simultaneously and transferring them to a second similar geometric array, including carrying and aligning means for maintaining a transfer means in superposed relationship with respect and for raising and lowering the transfer means into and out of proximity to said colonies or plaques, and (c) a subsystem for intially establishing such subarrays by transfer from a randomly spread pattern of colonies or plaques of bacteriophage.

US Patent:

57123799, Jan 27, 1998

Filed:

Jun 7, 1996

Appl. No.:

8/660275

Inventors:

Eric H. Davidson - Pasadena CA

Assignee:

California Institute of Technology - Pasadena CA

International Classification:

C07H 2104
C12P 2102

US Classification:

536 234

Abstract:

The present invention is directed to methods and compositions useful for altering the transcriptional expression of genes in eukaryotic cells. The invention employs novel antibody derivative molecules which function to recognize and bind to specific cis-regulatory DNA sequence elements of a eukaryotic gene. When two antibody derivative molecules are bound to adjacent cis-regulatory DNA sequence elements of a gene, those molecules may interact to form an antibody binding site which is capable of recognizing and binding to a transcription factor protein for the target gene, thereby affecting the functionality of that transcription factor protein and, in turn, the transcriptional activity of the gene. Also provided herein are isolated nucleic acids encoding the novel antibody derivative molecules of the present invention and expression vectors comprising those nucleic acids.

US Patent:

59945125, Nov 30, 1999

Filed:

Jul 20, 1998

Appl. No.:

9/118845

Inventors:

Eric H. Davidson - Pasadena CA

Assignee:

California Institute of Technology - Pasadena CA

International Classification:

C07K 1646

US Classification:

5303873

Abstract:

The present invention is directed to methods and compositions useful for altering the transcriptional expression of genes in eukaryotic cells. The invention employs novel antibody derivative molecules which function to recognize and bind to specific cis-regulatory DNA sequence elements of a eukaryotic gene. When two antibody derivative molecules are bound to adjacent cis-regulatory DNA sequence elements of a gene, those molecules may interact to form an antibody binding site which is capable of recognizing and binding to a transcription factor protein for the target gene, thereby affecting the functionality of that transcription factor protein and, in turn, the transcriptional activity of the gene. Also provided herein are isolated nucleic acids encoding the novel antibody derivative molecules of the present invention and expression vectors comprising those nucleic acids.