Abstract: Provided herein is technology relating to detecting nucleic acids in a sample and particularly, but not exclusively, to systems and methods related to random access primer pair libraries that are used to configure or customize assays for nucleic acid detection.
Abstract: The invention provides methods for extraction of fungal (e.g., yeast spp., filamentous fungal spp.) nucleic acid (e.g., DNA, RNA) from a sample (e.g., be human or veterinary clinical or research samples, agricultural samples, agricultural commodity samples, food products, or environmental samples). In some embodiments, the present invention provides enhanced nucleic acid extraction from samples comprising fungal cell(s) wherein enzymatic (e.g., lysostaphin treatment, lyticase treatment) sample treatment is performed in combination with mechanical (e.g., bead beating) sample treatment.
Type:
Application
Filed:
September 23, 2011
Publication date:
December 5, 2013
Applicant:
IBIS BIOSCIENCES, INC.
Inventors:
Gerard Gundling, Thomas Laffler, Cristina A. Ivy, Lendell Cummins
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:
March 5, 2007
Date of Patent:
October 22, 2013
Assignee:
Ibis Biosciences, Inc.
Inventors:
David J. Ecker, Richard H. Griffey, Rangarajan Sampath, Steven Hofstadler, John McNeil, Stanley T. Crooke, James C. Hannis
Abstract: The present invention provides integrated sample preparation systems and stabilized enzyme mixtures. In particular, the present invention provides microfluidic cards configured for processing a sample and generating DNA libraries that are suitable for use in sequencing methods (e.g., next generation sequencing methods) or other suitable nucleic acid analysis methods. The present invention also provides stabilized enzyme mixtures containing an enzyme (e.g., an enzyme used in whole genome amplification), BSA, and a sugar. Such enzyme mixtures may be lyophilized and stored at room temperature without significant loss of enzyme activity for months.
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.
Type:
Grant
Filed:
November 11, 2009
Date of Patent:
October 8, 2013
Assignee:
Ibis Biosciences, Inc.
Inventors:
David J. Ecker, Steven A. Hofstadler, Thomas A. Hall, 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:
Grant
Filed:
September 16, 2009
Date of Patent:
October 8, 2013
Assignee:
Ibis Biosciences, Inc.
Inventors:
Steven A. Hofstadler, Jared J. Drader, Jose R. Gutierrez, Rex O. Bare, Robert D. Miller, Jeffrey C. Smith
Abstract: The present invention provides compositions, kits and methods for rapid identification and quantification of sepsis-causing bacteria by molecular mass and base composition analysis.
Type:
Grant
Filed:
May 25, 2007
Date of Patent:
October 1, 2013
Assignee:
Ibis Biosciences, Inc.
Inventors:
Thomas A. Hall, Rangarajan Sampath, Vanessa Harpin, Steven A. Hofstadler, Yun Jiang
Abstract: Systems, computer program products, and methods useful for handling or managing microplates are provided.
Type:
Grant
Filed:
September 16, 2009
Date of Patent:
September 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, Kevin S. Oberkramer, Ronald K. Bergold
Abstract: Oligonucleotide primers and compositions and kits containing the same for rapid identification of orthopoxviruses by amplification of a segment of viral nucleic acid followed by molecular mass analysis are provided.
Type:
Application
Filed:
May 7, 2013
Publication date:
September 12, 2013
Applicant:
IBIS BIOSCIENCES, INC.
Inventors:
Rangarajan Sampath, Thomas A. Hall, David J. Ecker, Steven A. Hofstadler
Abstract: The present invention provides a method for rapid solution capture purification of nucleic acids for subsequent analysis by electrospray mass spectrometry which is efficient and cost-effective relative to existing methods. The present invention also provides kits useful for practicing rapid solution capture of nucleic acids so that purified samples are in condition for analysis by electrospray mass spectrometry.
Type:
Grant
Filed:
April 16, 2012
Date of Patent:
July 2, 2013
Assignee:
Ibis Biosciences, Inc.
Inventors:
Steven A. Hofstadler, Lendell L. Cummins
Abstract: The present invention provides integrated sample preparation systems and stabilized enzyme mixtures. In particular, the present invention provides microfluidic cards configured for processing a sample and generating DNA libraries that are suitable for use in sequencing methods or other suitable nucleic acid analysis methods. The present invention also provides stabilized enzyme mixtures containing an enzyme, BSA, and a sugar. Such enzyme mixtures may be lyophilized and stored at room temperature without significant loss of enzyme activity for months.
Abstract: The present invention provides compositions, kits and methods for rapid identification and quantification of adventitious contaminant viruses by molecular mass and base composition analysis.
Abstract: The methods described herein generally relate to characterization of large analytes, such as biomolecules, by molecular mass analysis. Specifically, the methods are directed to molecular mass analysis of singly- or multiply-charged ions by selective ion filtering carried out by a digital thresholding process.
Type:
Application
Filed:
May 7, 2012
Publication date:
April 18, 2013
Applicant:
IBIS BIOSCIENCES, INC.
Inventors:
Steven A. Hofstadler, Jared J. Drader, Amy L. Schink
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:
Grant
Filed:
March 17, 2008
Date of Patent:
March 26, 2013
Assignee:
Ibis Biosciences, Inc.
Inventors:
Steven A. Hofstadler, Thomas A. Hall, David J. Ecker, Lawrence B. Blyn, Mark W. Eshoo, Vivek Samant, Neill White
Abstract: The present invention provides compositions, kits and methods for rapid identification and quantification of bacteria by molecular mass and base composition analysis.
Type:
Grant
Filed:
March 7, 2007
Date of Patent:
March 12, 2013
Assignee:
Ibis Biosciences, Inc.
Inventors:
Rangarajan Sampath, Thomas A. Hall, David J. Ecker, Lawrence Blyn
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:
August 27, 2012
Publication date:
March 7, 2013
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 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 31, 2007
Date of Patent:
February 19, 2013
Assignee:
Ibis Bioscience, Inc.
Inventors:
David J. Ecker, Richard H. Griffey, Rangarajan Sampath, Steven A. Hofstadler, John McNeil, Stanley T. Crooke
Abstract: The present invention relates generally to strain typing of Escherichia coli TY2482 and/or LB226692, and provides methods, compositions and kits useful for this purpose when combined, for example, with molecular mass or base composition analysis. In particular embodiments, a genetic detection assay (e.g., SNP detection assay, sequencing, etc.) is used to identify mutations in the aggregative adherence fimbria I gene cluster fimbrial subunit (aggA) gene to identify the TY2482 strain, including mutations at position 103, 158, 188, 191, 197, and 271.
Type:
Application
Filed:
June 8, 2012
Publication date:
December 13, 2012
Applicant:
IBIS BIOSCIENCES, INC.
Inventors:
Christian Massire, Rangarajan Sampath, Feng Li, Roberta Housley
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:
Application
Filed:
May 2, 2012
Publication date:
November 8, 2012
Applicant:
IBIS BIOSCIENCES, INC.
Inventors:
Jared J. Drader, Gordon Bruce Collier, Steven A. Hofstadler
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:
February 13, 2007
Date of Patent:
October 30, 2012
Assignee:
Ibis Bioscience, Inc.
Inventors:
David J. Ecker, Richard H. Griffey, Rangarajan Sampath, Steven A. Hofstadler, John McNeil, Stanley T. Crooke