David E Root

US Patent:

6943009, Sep 13, 2005

Filed:

May 15, 2002

Appl. No.:

10/146831

Inventors:

William J. Lacey - North Andover MA, US
Gregory Mathus - Concord MA, US
David M. Root - Westford MA, US
John A. Ryan - Clinton MA, US

Assignee:

Corning Incorporated - Corning NY

International Classification:

C12M001/12

US Classification:

4352975, 4353052, 422101, 422102

Abstract:

A high-throughput cell or tissue culture apparatus, which is configurable to an industry-standard well plate format, is provided. The apparatus comprises a number of vessels, which may be suspended in wells of a plate. Each vessel has at least one sidewall defining a first opening and a second opening, each of predetermined cross-sectional area. The second opening has an inner cross-sectional area greater than either the inner cross-sectional area of the first opening or a cross-sectional area in a horizontal plane between the first and second openings. A relatively large substrate area is provided in each vessel for supporting tissue cultures in a fluid medium.

US Patent:

20040044063, Mar 4, 2004

Filed:

Jun 2, 2003

Appl. No.:

10/453143

Inventors:

Brent Stockwell - Boston MA, US
David Root - Brookline MA, US

International Classification:

A61K031/404

US Classification:

514/418000

Abstract:

This invention relates to therapies for diseases involving splicing defects, such as spinal muscular atrophy (SMA), and methods to identify compounds for treating this disease. The invention specifically provides for therapies comprised of small molecule compounds identified by cell-based high-throughput screening assays. These assays utilize engineered splicing constructs that fuse pre-mRNA fragments to a reporter gene. The fragments contain exons and at least one intron of a gene mutated in such a way to cause disease. Additionally, the invention provides for methods to monitor the effects of drugs on splicing and gene expression in vivo, in transgenic animals.

US Patent:

20070141594, Jun 21, 2007

Filed:

Oct 11, 2006

Appl. No.:

11/546019

Inventors:

Biao Luo - Lexington MA, US
David Root - Brookline MA, US
Xiaoping Yang - Brookline MA, US
Gregory Hinkle - Plymouth MA, US

International Classification:

C40B 40/08
C40B 50/06

US Classification:

435006000, 435091200

Abstract:

Described herein is a method of cloning synthetic oligos (including in situ synthesized oligos) into an (one or more) expression vector for library (e.g., shRNA library) production. The oligos are synthesized with one portion of the first stem of the hairpin, followed by a first loop sequence, the complete second stem, a second loop sequence, and finished with the remaining portion of the first stem of the hairpin. The two portions of the first stem anneal to the second stem, juxtaposing the 5′ end close to the 3′ end of the oligo. The methods described herein selected for hairpins with perfectly base-paired stems. After annealing, a ligase is added to the annealed oligos and the base-paired hairpins are preferentially annealed, and ligated, creating closed circular oligos. The now circularized hairpins served as templates for rolling circle amplification using a polymerase with high processivity. One or more primers complementary to the two strands of the amplified double stranded circular hairpins initiate the rolling circle amplification in the presence of a polymerase. Using primers (e.g., a sense and antisense primer), the rolling circle amplification yields double stranded hairpin sequences. These can be digested (e.g., using restriction enzymes) to produce a double-stranded hairpin fragment encoding a single hairpin. The fragment can be cloned into an appropriately digested vector for a variety of uses including expression.

US Patent:

20080166270, Jul 10, 2008

Filed:

Jan 23, 2008

Appl. No.:

12/018600

Inventors:

Jean I. Montagu - Brookline MA, US
Roger Dowd - Natick MA, US
David Root - Chelmsford MA, US

International Classification:

B01J 19/00

US Classification:

422102

Abstract:

An immobilizing device for biological material comprises a rigid support () carrying a substrate layer (′) of polymer having biological immobilizing properties, e.g. for amino and nucleic acids. Substantially solid ultra-thin substrate layers (′) having a thickness less than about 5 micron, preferably between about 0.1 and 0.5 micron, and micro-porous, ultra-thin substrate layers (′) having a thickness less than about 5 micron, preferably less than 3 micron, 2 or 1 micron are shown, which may be segmented by isolating moats M. The substrate layer is on a microscope slide (), round disc (), bio-cassette, at the bottom of a well of a multiwell plate, and as a coating inside a tube. Fluorescence or luminescence intensity and geometric calibration spots () are shown. Reading is enhanced by the intensity calibration spots () to enable normalization of readings under uneven illumination conditions, as when reading by dark field, side illumination mode. The reference spots are shown being printed simultaneously with printing an array of biological spots or with the same equipment. Methods of forming layers of the device include controlled drawing from a bath of coating composition and drying, and spinning of C-D shaped substrates. Post-forming treatment is shown by corona treatment and radiation. Adherent metal oxides (), silica-based materials and other materials are used to unite layers of the composite. In multiwell plates the oxide promotes joining of a bottom plate (′) and upper, well-defining structure () of dissimilar material. The oxides () also provide beneficial opacity to prevent light entering the glass support, for applying potential to the substrate, etc.

US Patent:

20090031435, Jan 29, 2009

Filed:

Nov 29, 2007

Appl. No.:

11/947589

Inventors:

Brent R. Stockwell - Boston MA, US
David E. Root - Brookline MA, US

International Classification:

A61K 31/4035
A61K 31/555
A61K 31/35
A61K 31/44
A61K 31/545
A61K 31/025
G01N 33/00
C12Q 1/68
G06Q 50/00

US Classification:

800 3, 514416, 514188, 514456, 514283, 514201, 514766, 435 6, 705 2

Abstract:

This invention relates to therapies for diseases involving splicing defects, such as spinal muscular atrophy (SMA), and methods to identify compounds for treating this disease. The invention specifically provides for therapies comprised of small molecule compounds identified by cell-based high-throughput screening assays. These assays utilize engineered splicing constructs that fuse pre-mRNA fragments to a reporter gene. The fragments contain exons and at least one intron of a gene mutated in such a way to cause disease. Additionally, the invention provides for methods to monitor the effects of drugs on splicing and gene expression in vivo, in transgenic animals.

US Patent:

20100311614, Dec 9, 2010

Filed:

Jun 15, 2010

Appl. No.:

12/815832

Inventors:

Jean I. Montagu - Brookline MA, US
Roger Dowd - Natick MA, US
David Root - Chelmsford MA, US

Assignee:

AVANTRA BIOSCIENCES CORPORATION - Boston MA

International Classification:

C40B 40/02
B05D 3/06
B05D 3/02
B05D 1/18
C40B 40/00
C40B 40/06
C40B 40/08
C40B 40/10

US Classification:

506 14, 427533, 427551, 427553, 427224, 427384, 4274301, 506 13, 506 16, 506 17, 506 18, 506 40

Abstract:

An immobilizing device for biological material comprises a rigid support () carrying a substrate layer (′) of polymer having biological immobilizing properties, e.g. for amino and nucleic acids. Substantially solid ultra-thin substrate layers (′) having a thickness less than about 5 micron, preferably between about 0.1 and 0.5 micron, and microporous, ultra-thin substrate layers (′) having a thickness less than about 5 micron, preferably less than 3 micron, 2 or 1 micron are shown, which may be segmented by isolating moats M. The substrate layer is on a microscope slide (), round disc (), bio-cassette, at the bottom of a well of a multiwell plate, and as a coating inside a tube. Fluorescence or luminescence intensity and geometric calibration spots () are shown. Reading is enhanced by the intensity calibration spots () to enable normalization of readings under uneven illumination conditions, as when reading by dark field, side illumination mode. The reference spots are shown being printed simultaneously with printing an array of biological spots or with the same equipment. Methods of forming layers of the device include controlled drawing from a bath of coating composition and drying, and spinning of C-D shaped substrates. Post-forming treatment is shown by corona treatment and radiation. Adherent metal oxides (), silica-based materials and other materials are used to unite layers of the composite. In multiwell plates the oxide promotes joining of a bottom plate (′) and upper, well-defining structure () of dissimilar material. The oxides () also provide beneficial opacity to prevent light entering the glass support, for applying potential to the substrate, etc.

US Patent:

20120129713, May 24, 2012

Filed:

Oct 13, 2011

Appl. No.:

13/272980

Inventors:

Jean I. Montagu - Brookline MA, US
Roger Dowd - Natick MA, US
David Root - Chelmsford MA, US

International Classification:

C40B 30/04
B05D 1/36
C40B 60/12
B05D 1/18

US Classification:

506 9, 4274301, 427404, 506 39

Abstract:

An immobilizing device for biological material comprises a rigid support () carrying a substrate layer () of polymer having biological immobilizing properties, e.g. for amino and nucleic acids. Substantially solid ultra-thin substrate layers () having a thickness less than about 5 micron, preferably between about 0.1 and 0.5 micron, and micro-porous, ultra-thin substrate layers () having a thickness less than about 5 micron, preferably less than 3 micron, 2 or 1 micron are shown, which may be segmented by isolating moats M. The substrate layer is on a microscope slide (), round disc (), bio-cassette, at the bottom of a well of a multiwell plate, and as a coating inside a tube.

US Patent:

48957062, Jan 23, 1990

Filed:

Apr 28, 1988

Appl. No.:

7/187083

Inventors:

David Root - Lexington MA
George Lyman - Kennebunk ME

Assignee:

Costar Corporation - Cambridge MA

International Classification:

B01L 300
G01N 118

US Classification:

422102

Abstract:

A filter strip and composite assemblies for filtering microliter quantities of fluids wherein a linear array of wells having open top and bottom ends are connected by frangible webs in spaced-apart relation with discrete filter membranes closing the bottom ends of each well. Tabs are provided on the ends of the filter strip for holding the same and supporting the strip in a rectangular holder having alphanumeric designations for identifying each well in a plurality of such filter strips contained within the holder. The filter strip may be used in a vacuum manifold for applying a pressure differential across the filter membrane and directing the filtrate into an aligned aperture of a closed bottom well of an array of wells held within the manifold. Alternatively, the filter strip may be used with a transfer plate for directing the filtrate from each well of the filter strip to an aligned well of a closed bottom array of wells. Another composite assembly includes a pressure manifold for applying an increased pressure above the membranes.