Patents by Inventor Jaakko Kurkela
Jaakko Kurkela has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20230323478Abstract: The present invention provides a nucleic acid amplification based method for detecting a hypervirulent Clostridium difficile strain in a biological sample. The present invention is based on the use of oligonucleotide primers and probes specific to negative and positive markers in hypervirulent Clostridium difficile genome.Type: ApplicationFiled: December 22, 2022Publication date: October 12, 2023Applicant: Mobidiag LtdInventors: Juha Kirveskari, Jaakko Kurkela
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Patent number: 11566294Abstract: The present invention provides a nucleic acid amplification based method for detecting a hypervirulent Clostridium difficile strain in a biological sample. The present invention is based on the use of oligonucleotide primers and probes specific to negative and positive markers in hypervirulent Clostridium difficile genome.Type: GrantFiled: December 18, 2015Date of Patent: January 31, 2023Assignee: Mobidiag Ltd.Inventors: Juha Kirveskari, Jaakko Kurkela
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Publication number: 20190345540Abstract: The present invention provides a nucleic acid amplification based method for detecting a hypervirulent Clostridium difficile strain in a biological sample. The present invention is based on the use of oligonucleotide primers and probes specific to negative and positive markers in hypervirulent Clostridium difficile genome.Type: ApplicationFiled: December 18, 2015Publication date: November 14, 2019Inventors: Juha Kirveskari, Jaakko Kurkela
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Publication number: 20180314789Abstract: A technique for analyzing a melt curve characterizing the melt of a solution comprising one or more populations of nucleic acid molecules and a constant number of fluorophores of at least first type is provided.Type: ApplicationFiled: February 26, 2018Publication date: November 1, 2018Inventors: Tuomo Von Lerber, Jaakko Kurkela, David Cohen
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Publication number: 20180136150Abstract: Described herein are methods and systems for analyzing and visualizing HRM data from a double-stranded nucleic acid. The HRM data is generally characterized by a plurality of data points each including a signal value associated with the concentration of a double-stranded nucleic acid in a sample and a temperature value associated with a the temperature of the sample. Embodiments of the invention analyze the HRM curves from samples using the first negative derivative of the HRM curve or a virtual standard. The first negative derivative plot method may be used to identify the melting temperature of a homogenous double-stranded nucleic acid in a sample, as well as the presence and melting temperature of heterogeneous double-stranded nucleic acids in the sample. Data points associated with the melting temperature are plotted on a scatter plot for analysis. The virtual standard allows for visualization of HRM data across data sets.Type: ApplicationFiled: January 15, 2018Publication date: May 17, 2018Inventors: Jorma MUSTOLA, Ville VAHERVUORI, Ian KAVANAGH, David COHEN, Jaakko KURKELA, Ossian SARIS, Charles ANDRE
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Patent number: 9617588Abstract: Polymorphisms are present throughout an organism's genome, and understanding which alleles are present in a particular organism's genome can be advantageous. When probing the identity of these alleles, one must minimize incorrect readings due to inefficiencies in the system. In hydrolysis probe applications, these inefficiencies may be due to over-activity of an exonuclease functionality that excises nucleotides from probes that are only partially, complementary to a region of a target. The present invention provides a mixture that contains a plurality of polymerases including one that has a 5??3? exonuclease functionality and one that lacks or substantially lacks it, each in a sufficient relative amount and concentration to increase efficiencies of the system.Type: GrantFiled: October 4, 2011Date of Patent: April 11, 2017Assignee: Thermo Fisher Scientific Baltics UABInventor: Jaakko Kurkela
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Publication number: 20160312268Abstract: The invention relates to a method of preparing a reaction mixture for Polymerase Chain Reaction (PCR) assay and a solution set for PCR. The method comprises providing a sample solution comprising a biological sample to be amplified in said PCR assay and first colorant providing the solution a first color, providing a reagent solution comprising at least one other substance required for performing said assay and second colorant providing the solution a second color different from the first color, and mixing the sample solution and the first reagent solution for providing a mixed solution to be subjected to the PCR process, the mixed solution having, due to said first and second colorants, a third color different from the first and second colors. The invention significantly aids in pipetting PCR assays.Type: ApplicationFiled: April 27, 2016Publication date: October 27, 2016Applicant: Thermo Fisher Scientific Baltics UABInventors: Jaakko KURKELA, Katja EKLIN, Sanna UUSIVIRTA
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Patent number: 9422604Abstract: The invention relates to a sample processing apparatus comprising a holder for a microtiter plate comprising a plurality of microwells, optical measurement unit for measuring optical responses of samples dosed to the microwells, and a computing unit configured to analyze the optical responses in order to detect dosing failures in said plurality of microwells, and if a dosing failure has been detected in one or more of the microwells, to communicate the existence of the dosing failure to a user of the apparatus through signaling means or to store data indicative of the dosing failure to data storage means for further use. In particular, the invention relates to detecting dosing failures in before, during and after a PCR process.Type: GrantFiled: April 1, 2011Date of Patent: August 23, 2016Assignee: Thermo Fisher Scientific Baltics UABInventors: Jukka Tuunanen, Jaakko Kurkela, Katja Eklin
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Patent number: 9416417Abstract: The invention relates to a method of preparing a reaction mixture for Polymerase Chain Reaction (PCR) assay and a solution set for PCR. The method comprises providing a sample solution comprising a biological sample to be amplified in said PCR assay and first colorant providing the solution a first color, providing a reagent solution comprising at least one other substance required for performing said assay and second colorant providing the solution a second color different from the first color, and mixing the sample solution and the first reagent solution for providing a mixed solution to be subjected to the PCR process, the mixed solution having, due to said first and second colorants, a third color different from the first and second colors. The invention significantly aids in pipetting PCR assays.Type: GrantFiled: March 3, 2014Date of Patent: August 16, 2016Assignee: Thermo Fisher Scientific Baltics UABInventors: Jaakko Kurkela, Katja Eklin, Sanna Uusivirta
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Publication number: 20160085908Abstract: A method of high resolution melting curve analysis for characterizing nucleic acid molecules such as PCR products having a distinct Tm using fluorescence is provided. The technique comprises modeling the raw melting curve data as a sum of at least two signal components, the first signal component representing the light intensity emitted by unbound/free fluorophores and the one or more second signal components representing the combined light intensity emitted by fluorophores bound to double stranded DNA. Numerical analysis is used to determine the values of the different components contributing to the total signal such that the model matches the raw fluorescence data as closely as possible. The method enables an improved resolution of mixtures of target nucleic acids even at non-saturating dye concentrations because it takes into account the effect of redistribution of intercalating dye from low-temperature duplexes to duplexes that melt at higher temperatures.Type: ApplicationFiled: April 23, 2013Publication date: March 24, 2016Inventors: Tuomo Von Lerber, Jaakko Kurkela, David Cohen
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Publication number: 20140273254Abstract: Methods and systems are described for quantifying the methylation status of nucleic acids in a sample utilizing standardized curves derived from methylation-sensitive HRM data. The standardized curves are generated from HRM curves from a plurality of samples, each sample having a known but different methylation status. In one embodiment, the first negative derivative of each HRM curve from the known samples is plotted and a first value corresponding with a first melt peak and a second value corresponding with a second melt peak from the negative derivative plots are identified. The slope of a line connecting the first and second values for each sample is calculated and used to identify a slope data point that is plotted to generate the standardized curve. In another embodiment, a threshold line that intersects the plurality of HRM curves is generated and the standardized curve is generated from the intersection data points.Type: ApplicationFiled: March 14, 2014Publication date: September 18, 2014Applicant: Thermo Fisher Scientific OyInventor: Jaakko Kurkela
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Publication number: 20140178880Abstract: The invention relates to a method of preparing a reaction mixture for Polymerase Chain Reaction (PCR) assay and a solution set for PCR. The method comprises providing a sample solution comprising a biological sample to be amplified in said PCR assay and first colorant providing the solution a first color, providing a reagent solution comprising at least one other substance required for performing said assay and second colorant providing the solution a second color different from the first color, and mixing the sample solution and the first reagent solution for providing a mixed solution to be subjected to the PCR process, the mixed solution having, due to said first and second colorants, a third color different from the first and second colors. The invention significantly aids in pipetting PCR assays.Type: ApplicationFiled: March 3, 2014Publication date: June 26, 2014Applicant: Thermo Fisher Scientific Baltics UABInventors: Jaakko KURKELA, Katja Eklin, Sanna Uusivirta
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Patent number: 8663925Abstract: The invention relates to a method of preparing a reaction mixture for Polymerase Chain Reaction (PCR) assay and a solution set for PCR. The method comprises providing a sample solution comprising a biological sample to be amplified in said PCR assay and first colorant providing the solution a first color, providing a reagent solution comprising at least one other substance required for performing said assay and second colorant providing the solution a second color different from the first color, and mixing the sample solution and the first reagent solution for providing a mixed solution to be subjected to the PCR process, the mixed solution having, due to said first and second colorants, a third color different from the first and second colors. The invention significantly aids in pipetting PCR assays.Type: GrantFiled: October 4, 2010Date of Patent: March 4, 2014Assignee: Thermo Fisher Scientific Baltics UABInventors: Jaakko Kurkela, Katja Eklin, Sanna Uusivirta
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Publication number: 20130338928Abstract: Described herein are methods and systems for analyzing and visualizing HRM data from a double-stranded nucleic acid. The HRM data is generally characterized by a plurality of data points each including a signal value associated with the concentration of a double-stranded nucleic acid in a sample and a temperature value associated with a the temperature of the sample. Embodiments of the invention analyze the HRM curves from samples using the first negative derivative of the HRM curve or a virtual standard. The first negative derivative plot method may be used to identify the melting temperature of a homogenous double-stranded nucleic acid in a sample, as well as the presence and melting temperature of heterogeneous double-stranded nucleic acids in the sample. Data points associated with the melting temperature are plotted on a scatter plot for analysis. The virtual standard allows for visualization of HRM data across data sets.Type: ApplicationFiled: March 13, 2013Publication date: December 19, 2013Applicant: Thermo Fisher Scientific OyInventors: Jorma Mustola, Ville Vahervuori, Ian Kavanagh, David Cohen, Jaakko Kurkela, Ossian Saris, Chas Andre
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Publication number: 20120219957Abstract: The invention relates to a method of preparing a reaction mixture for Polymerase Chain Reaction (PCR) assay and a solution set for PCR. The method comprises providing a sample solution comprising a biological sample to be amplified in said PCR assay and first colorant providing the solution a first color, providing a reagent solution comprising at least one other substance required for performing said assay and second colorant providing the solution a second color different from the first color, and mixing the sample solution and the first reagent solution for providing a mixed solution to be subjected to the PCR process, the mixed solution having, due to said first and second colorants, a third color different from the first and second colors. The invention significantly aids in pipetting PCR assays.Type: ApplicationFiled: October 4, 2010Publication date: August 30, 2012Applicant: Finnzymes OyInventors: Jaakko Kurkela, Katja Eklin, Sanna Uusivirta
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Publication number: 20120082995Abstract: The present invention is directed to a method for quantitative PCR amplification of deoxyribonucleic acids (DNA) from a sample containing PCR inhibitors such as biological, clinical or environmental samples. In the method of the invention an inhibitor-tolerant DNA polymerase is used in a pre-amplification step to increase the copy number of DNA from these samples. In the pre-amplification step, the PCR reaction preferably comprises at least the same amount of effective PCR inhibitors as a reaction with 1% (v/v) human blood. The pre-amplified sample is subsequently diluted in order to dilute inhibitory substances remaining in the sample and thus rendering possible to use an aliquot of the diluted sample in quantitative PCR, which is very sensitive for these inhibitors.Type: ApplicationFiled: June 28, 2010Publication date: April 5, 2012Inventor: Jaakko Kurkela
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Publication number: 20120082981Abstract: Polymorphisms are present throughout an organism's genome, and understanding which alleles are present in a particular organism's genome can be advantageous. When probing the identity of these alleles, one must minimize incorrect readings due to inefficiencies in the system. In hydrolysis probe applications, these inefficiencies may be due to over-activity of an exonuclease functionality that excises nucleotides from probes that are only partially, complementary to a region of a target. The present invention provides a mixture that contains a plurality of polymerases including one that has a 5??3? exonuclease functionality and one that lacks or substantially lacks it, each in a sufficient relative amount and concentration to increase efficiencies of the system.Type: ApplicationFiled: October 4, 2011Publication date: April 5, 2012Applicant: Finnzymes OyInventor: Jaakko Kurkela
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Publication number: 20110251080Abstract: The invention relates to a sample processing apparatus comprising a holder for a microtiter plate comprising a plurality of microwells, optical measurement unit for measuring optical responses of samples dosed to the microwells, and a computing unit configured to analyze the optical responses in order to detect dosing failures in said plurality of microwells, and if a dosing failure has been detected in one or more of the microwells, to communicate the existence of the dosing failure to a user of the apparatus through signaling means or to store data indicative of the dosing failure to data storage means for further use. In particular, the invention relates to detecting dosing failures in before, during and after a PCR process.Type: ApplicationFiled: April 1, 2011Publication date: October 13, 2011Applicant: FINNZYMES OYInventors: Jukka TUUNANEN, Jaakko Kurkela, Katja Eklin