Abstract: The present invention relates generally to methods of determining base compositions for PCR products (e.g., RT PCR products, (rt) RT-PCR products, etc.). In particular, the present invention provides base-composition determination of PCR products containing up to five different nucleobases (e.g., A, C, G, T, U) and/or significant levels of non-templated adenylation.
Abstract: The present invention relates generally to the field of investigational bioinformatics and more particularly to secondary structure defining databases. The present invention further relates to methods for interrogating a database as a source of molecular masses of known bioagents for comparing against the molecular mass of an unknown or selected bioagent to determine either the identity of the selected bioagent, and/or to determine the origin of the selected bioagent. The identification of the bioagent is important for determining a proper course of treatment and/or irradication of the bioagent in such cases as biological warfare. Furthermore, the determination of the geographic origin of a selected bioagent will facilitate the identification of potential criminal identity.
Type:
Grant
Filed:
October 29, 2012
Date of Patent:
December 30, 2014
Assignee:
Ibis Biosciences, Inc.
Inventors:
David J. Ecker, Richard H. Griffey, Rangarajan Sampath, Steven A. Hofstadler, John McNeil, Stanley T. Crooke
Abstract: The present invention relates to methods and compositions for tagging, amplifying, purifying, and or characterizing of ribonucleic acid (RNA) in a sample. In particular, methods are provided for preparing RNA from a sample for subsequent analysis.
Abstract: The present invention provides methods and primer pairs for rapid, high-resolution forensic analysis of DNA and STR-typing by using amplification and mass spectrometry, determining the molecular masses and calculating base compositions of amplification products and comparing the molecular masses with the molecular masses of theoretical amplicons indexed in a database.
Type:
Grant
Filed:
February 25, 2008
Date of Patent:
October 28, 2014
Assignee:
IBIS Biosciences, Inc.
Inventors:
Thomas A. Hall, Steven A. Hofstadler, Kristin Sannes-Lowery
Abstract: Cartridges useful for mixing materials, such as fluidic materials are provided. A cartridge typically includes a body structure having surfaces that define a cavity with upper and lower portions. A rotatable member generally extends along a horizontal axis in the upper portion of the cavity. One or more protrusions typically extend outward from the rotatable member and into the lower portion of the cavity, and are configured to mix the material when the material is disposed in the cavity. Related mixing stations, systems, kits, and methods are also provided.
Type:
Application
Filed:
October 7, 2013
Publication date:
October 16, 2014
Applicant:
IBIS BIOSCIENCES, INC.
Inventors:
Steven A. Hofstadler, Jared J. Drader, Jose R. Gutierrez, Rex O. Bare, Robert D. Miller, Jeffrey C. Smith
Abstract: Provided herein is technology relating to detecting nucleic acids in a sample and particularly, but not exclusively, to systems and methods related to panels that are used to evaluate sequencing efficacy.
Abstract: Provided herein are compositions and methods for the alteration of neuronal methylation by synthetic piRNAs or by alteration of piRNA function. Such alterations find use in the regulation and control of neural gene expression and concomitant neural functions. Further provided herein are systems and methods for the identification of target sites for regulation by piRNAs.
Type:
Application
Filed:
March 14, 2014
Publication date:
September 18, 2014
Applicant:
IBIS Biosciences, Inc.
Inventors:
David J. Ecker, Todd P. Michael, Lendell L. Cummins, Mark W. Eshoo, Stanley T. Motley, Danny M. Chou
Abstract: The present invention provides methods of: identifying pathogens in biological samples from humans and animals, resolving a plurality of etiologic agents present in samples obtained from humans and animals, determining detailed genetic information about such pathogens or etiologic agents, and rapid detection and identification of bioagents from environmental, clinical or other samples.
Type:
Grant
Filed:
September 23, 2011
Date of Patent:
September 2, 2014
Assignee:
Ibis Biosciences, Inc.
Inventors:
David J. Ecker, Richard H. Griffey, Rangarajan Sampath, Steven A. Hofstadler, John McNeil, Stanley T. Crooke, Lawrence B. Blyn, Raymond Ranken, Thomas A. Hall
Abstract: Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to devices, methods, and systems for sequencing-by-synthesis using changes in pH to monitor base addition. In some embodiments the electrochemical hydrogen ion sensor is a microfabricated mixed metal oxide electrode and in some embodiments the electrochemical hydrogen ion sensor is a membrane electrode. Moreover, in some embodiments the device further comprises a reference electrode. Performing the sequencing reaction involves moving solutions and other fluids (e.g., samples, nucleotide solutions, wash solutions) into and out of the reaction vessel. Thus, in some embodiments, the device further comprises a tube or other transport mechanism or pathway attached to the reaction vessel.
Type:
Application
Filed:
August 3, 2012
Publication date:
August 28, 2014
Applicant:
IBIS BIOSCIENCES, INC.
Inventors:
Jeffrey Huff, Graham Davis, Mark Hayden, David J. Ecker, Dan Wang, Gordon Bruce Collier
Abstract: The present invention provides methods for rapid forensic investigations by identification of bioagents associated with biowarfare and acts of terrorism or crime. The methods are also useful for epidemiological investigations by genotyping of bioagents.
Type:
Grant
Filed:
October 31, 2007
Date of Patent:
August 26, 2014
Assignee:
Ibis Biosciences, Inc.
Inventors:
David J. Ecker, Richard H. Griffey, Rangarajan Sampath, Steven A. Hofstadler, John McNeil, Stanley T. Crooke, James C. Hannis
Abstract: There is a need for nucleic acid analysis which is both specific and rapid, and in which no nucleic acid sequencing is required. The present invention addresses this need, among others by providing a method of nucleic acid amplification of overlapping sub-segments of a nucleic acid followed by molecular mass measurement of resulting amplification products by mass spectrometry, and determination of the base compositions of the amplification products.
Abstract: Sample processing units useful for mixing and purifying materials, such as fluidic materials are provided. A sample processing unit typically includes a container configured to contain a sample comprising magnetically responsive particles, and one or more magnets that are in substantially fixed positions relative to the container. A sample processing unit also generally includes a conveyance mechanism configured to convey the container to and from a position that is within magnetic communication with the magnet, e.g., such that magnetically responsive particles with captured analytes can be retained within the container when other materials are added to and/or removed from the container. Further, a sample processing unit also typically includes a rotational mechanism that is configured to rotate the container, e.g., to effect mixing of sample materials disposed within the container. Related carrier mechanisms, sample processing stations, systems, and methods are also provided.
Type:
Application
Filed:
December 10, 2013
Publication date:
August 14, 2014
Applicant:
IBIS BIOSCIENCES, INC.
Inventors:
Steven A. Hofstadler, Jared J. Drader, Jose R. Gutierrez, Paul J. Gleason, Rex O. Bare, Robert D. Miller, Jeffrey C. Smith
Abstract: The present invention provides methods for rapid forensic analysis of mitochondrial DNA and methods for characterizing heteroplasmy of mitochondrial DNA, which can be used to assess the progression of mitochondrial diseases.
Type:
Grant
Filed:
October 30, 2007
Date of Patent:
August 12, 2014
Assignee:
Ibis Biosciences, Inc.
Inventors:
David J. Ecker, Richard H. Griffey, Rangarajan Sampath, Steven A. Hofstadler, John McNeil, Stanley T. Crooke, Lawrence Blyn, Thomas A. Hall, Yun Jiang, James C. Hannis, Neill White, Vivek Samant, Mark W. Eshoo, Jared James Drader
Abstract: The invention relates generally to sample ionization, and provides ionization probe assemblies, systems, computer program products, and methods useful for this purpose.
Type:
Grant
Filed:
January 3, 2012
Date of Patent:
August 5, 2014
Assignee:
Ibis BioSciences, Inc.
Inventors:
Steven A. Hofstadler, Jose R. Gutierrez, James C. Hannis, Jared J. Drader, Rex O. Bare, Jeffrey C. Smith, Paul J. Gleason, Jared Nathanson
Abstract: Systems, computer program products, and methods useful for handling or managing microplates are provided.
Type:
Application
Filed:
September 16, 2013
Publication date:
June 5, 2014
Applicant:
IBIS BIOSCIENCES, INC.
Inventors:
Steven A. Hofstadler, Jared J. Drader, Jose R. Gutierrez, Paul J. Gleason, Rex O. Bare, Robert D. Miller, Jeffrey C. Smith, Kevin S. Oberkramer, Ronald K. Bergold
Abstract: The present invention provides methods for the quantification of an unknown bioagent in a sample by amplification of nucleic acid of the bioagent, and concurrent amplification of a known quantity of a calibration polynucleotide from which are obtained a bioagent identifying amplicon and a calibration amplicon. Upon molecular mass analysis, mass and abundance data are obtained. The identity of the bioagent is then determined from the molecular mass of the bioagent identifying amplicon and the quantity of the identified bioagent in the sample is determined from the abundance data of the bioagent identifying amplicon and the abundance data of the calibration amplicon.
Type:
Application
Filed:
January 27, 2014
Publication date:
May 22, 2014
Applicant:
IBIS BIOSCIENCES, INC.
Inventors:
David J. Ecker, Rangarajan Sampath, Lawrence B. Blyn, Steven A. Hofstadler, Thomas A. Hall
Abstract: The present invention relates generally to the field of nucleic acid purification. In particular, provided herein are micro particles and micro particle clusters for selective anion exchange of nucleic acids, and methods and kits useful for this purpose.
Type:
Application
Filed:
July 2, 2013
Publication date:
January 9, 2014
Applicant:
IBIS BIOSCIENCES, INC.
Inventors:
Gregory Richmond, Jose R. Gutierrez, Steven A. Hofstadler
Abstract: Provided herein is technology relating to testing biological samples and particularly, but not exclusively, to devices, systems, and kits for performing multiple, simultaneous real-time assays on a sample in a single-use disposable format. For example, the technology relates to an apparatus that finds use, for example, for point-of-care diagnostics, including use at accident sites, emergency rooms, in surgery, in intensive care units, as well as for non-medical applications.
Type:
Grant
Filed:
May 2, 2012
Date of Patent:
December 24, 2013
Assignee:
Ibis Biosciences, Inc.
Inventors:
Jared J. Drader, Gordon Bruce Collier, Steven A. Hofstadler
Abstract: The present invention provides methods for rapid forensic analysis of mitochondrial DNA by amplification of a segment of mitochondrial DNA containing restriction sites, digesting the mitochondrial DNA segments with restriction enzymes, determining the molecular masses of the restriction fragments and comparing the molecular masses with the molecular masses of theoretical restriction digests of known mitochondrial DNA sequences stored in a database.
Type:
Application
Filed:
March 26, 2013
Publication date:
December 19, 2013
Applicant:
IBIS BIOSCIENCES, INC.
Inventors:
Steven A. Hofstadler, Thomas A. Hall, David J. Ecker, Lawrence B. Blyn, Mark W. Eshoo, Vivek Samant, Neill White
Abstract: Sample processing units useful for mixing and purifying materials, such as fluidic materials are provided. A sample processing unit typically includes a container configured to contain a sample comprising magnetically responsive particles, and one or more magnets that are in substantially fixed positions relative to the container. A sample processing unit also generally includes a conveyance mechanism configured to convey the container to and from a position that is within magnetic communication with the magnet, e.g., such that magnetically responsive particles with captured analytes can be retained within the container when other materials are added to and/or removed from the container. Further, a sample processing unit also typically includes a rotational mechanism that is configured to rotate the container, e.g., to effect mixing of sample materials disposed within the container. Related carrier mechanisms, sample processing stations, systems, and methods are also provided.
Type:
Grant
Filed:
August 27, 2012
Date of Patent:
December 17, 2013
Assignee:
Ibis Biosciences, Inc.
Inventors:
Steven A. Hofstadler, Jared J. Drader, Jose R. Gutierrez, Paul J. Gleason, Rex O. Bare, Robert D. Miller, Jeffrey C. Smith