Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Objections
Claim 1 is objected to because of the following informalities:
in line 29 “leackage” should be –leakage— [which would be similar to “leakage” in line 16]. Appropriate correction is required.
Claim 1 is objected to because of the following informalities:
In line 32, “ ),” should be deleted as being redunant—. Appropriate correction is required.
Claim 2 is objected to because of the following informalities:
in line 29 “leackage” should be –leakage—. Appropriate correction is required.
Claim 7 is objected to because of the following informalities:
in line 2 “leackage” should be –leakage—. Appropriate correction is required.
Claim 16 is objected to because of the following informalities:
in line 33 “leackage” should be –leakage—. Appropriate correction is required.
Claim 16, line 5 recites “A method”. This should be –a method--.
Claim 17 is objected to because of the following informalities:
in line 33 “leackage” should be –leakage—. Appropriate correction is required.
Claim 17, line 5 recites “A method”. This should be –a method--.
Claim 18 is objected to because of the following informalities:
in line 33 “leackage” should be –leakage—. Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-18 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites the following in lines 21-31:
“- correcting the donor-acceptor-labelled eFRET results based on the leakage coefficient (cik) and the direct excitation coefficient (cdirE);
wherein the first and/or the second eFRET results comprise respective measurement values of the
- emission of the acceptor after donor excitation (FDA(A)),
- emission of the acceptor after acceptor excitation (FAA(A)), and/or
- emission of the donor after donor excitation (FDD(D)),
- emission of the donor after acceptor excitation (FDA(D))
wherein said leackage coefficient (clk) is determined based on the ratio of FDA(D) and FDD(D); and said direct excitation coefficient (CdirE) is determined based on the ratio of FDA(A) and FAA(A);” (emphasis added).
Thus, lines 21-22 of claim 1 requires measuring values of FDA(D), FDD(D), FDA(A), and FAA(A), as these are required to obtain the leakage coefficient (cik) and the direct excitation coefficient (cdirE).
However, line 26 reciting “and/or”, which encompasses the alternative “or”, indicates that
measuring values of FDA(D), FDD(D), FDA(A), and FAA(A)” are not all required, but are alternatives.
Therefore lines 21-22 and line 26 contradict each other. Clarification is required.
Similarly, regarding claim 2, lines 21-22 of claim 2 requires measuring values of FDA(D), FDD(D), FDA(A), and FAA(A)” as these are required to obtain the leakage coefficient (cik) and the direct excitation coefficient (cdirE).
However, line 26 of claim 2 reciting “and/or”, which encompasses the alternative “or”, indicates
that measuring values of FDA(D), FDD(D), FDA(A), and FAA(A)” are not all required, but are alternatives.
Therefore lines 21-22 and line 26 contradict each other. Clarification is required.
Similarly, regarding claim 16, lines 25-26 of claim 16 requires measuring values of FDA(D), FDD(D), FDA(A), and FAA(A)” as these are required to obtain the leakage coefficient (cik) and the direct excitation coefficient (cdirE).
However, line 30 of claim 16 reciting “and/or”, which encompasses the alternative “or”,
indicates that measuring values of FDA(D), FDD(D), FDA(A), and FAA(A)” are not all required, but are alternatives.
Therefore lines 25-26 and line 30 contradict each other. Clarification is required.
Similarly, regarding claim 17, lines 25-26 of claim 16 requires measuring values of FDA(D), FDD(D), FDA(A), and FAA(A)” as these are required to obtain the leakage coefficient (cik) and the direct excitation coefficient (cdirE).
However, line 30 of claim 16 reciting “and/or”, which encompasses the alternative “or”,
indicates that measuring values of FDA(D), FDD(D), FDA(A), and FAA(A)” are not all required, but are alternatives.
Therefore lines 25-26 and line 30 contradict each other. Clarification is required.
Similarly, regarding claim 18, lines 25-26 of claim 16 requires measuring values of FDA(D), FDD(D), FDA(A), and FAA(A)” as these are required to obtain the leakage coefficient (cik) and the direct excitation coefficient (cdirE).
However, line 30 of claim 16 reciting “and/or”, which encompasses the alternative “or”,
indicates that measuring values of FDA(D), FDD(D), FDA(A), and FAA(A)” are not all required, but are alternatives.
Therefore lines 25-26 and line 30 contradict each other. Clarification is required.
Claim 3 recites in line 9 “preferably a fluorophore”. It is not clear if a fluorophore is required, given the term “preferably”. Clarification is requested.
Claim 5 recites in lines 5 and 8 “preferably”. It is not clear if the limitations that follow are required, given the term “preferably”. Clarification is requested.
Claim 6 recites in lines 2, 3and 6 “preferably”. It is not clear if the limitations that follow are required, given the term “preferably”. Clarification is requested.
Claim 7 recites in line 5 “preferably”. It is not clear if the limitations that follow are required, given the term “preferably”. Clarification is requested.
Claim 8 recites in lines 3, 5, and 7 “preferably”. It is not clear if the limitations that follow are required, given the term “preferably”. Clarification is requested.
Claim 15 recites in line 11 “preferably”. It is not clear if the limitations that follow are required, given the term “preferably”. Clarification is requested.
Claim 15 recites in lines 1-4, “A measurement system comprising a controller adapted for obtaining quantitative information on average donor-acceptor distance or on average donor-acceptor distance changes in accordance with claim 1, wherein said measurement system comprises:” (emphasis added).
It is not clear if the controller is part of the preamble or part of the body of the claim. That is, it is not clear if a controller is a required part of the measurement system. Clarification is required. For examination purposes, the claim is interpreted to require the controller.
Claim 15, line 1 recites “controller adapted for obtaining quantitative information on average donor-acceptor distance or on average donor-acceptor distance changes in accordance with claim 1”.
Applicant does not disclose an example of such a controller in the specification, and thus it is not clear as to what this limitation encompasses. Does it encompass a computer? Does it encompass a detector? Does it encompass a system that includes a computer, detector, vessels, other laboratory devices? For examination purposes, the limitation is interpreted to encompass anything that is capable of performing the recited use. However, clarification is required.
Claim 15, line 5 recites “means for accommodating vessels”. Applicant’s specification does not give any examples of a means for accommodating vessels, and thus it is not clear as to what this limitation means. However, for examination purposes, the limitation is interpreted to encompass anything that can accommodate, i.e., hold, vessels (any kind of vessels).
Claim 15, line 12 recites “means for performing an eFRET measurement”.
Paragraph 0180 discloses a “detector” generically. It appears that Applicant intends to refer to known detectors for FRET, and therefore “means for performing an eFRET measurement” is interpreted to refer to detectors for FRET known at the time of Applicant’s effective filing date. However, clarification is requested.
Claim 15, line 14 recites “control means adapted for controlling the means for accommodating the vessel; controlling the at least one light source…..controlling the at least one light detector….and controlling said means for performing the eFRET measurement”. Applicant’s specification does not give an example of the recited “control means”, and thus it is not clear as to what this limitation means. Does it encompass a computer? Does it encompass robotic arms? Does it encompass translational stages that can be moved? For examination purposes, the limitation is interpreted to encompass anything (such as a computer and electronics) that can control the recited limitations.
The remaining claims are rejected since they depend from one of the above-rejected claims without clarifying the vagueness set forth above.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
Claim 15, line 1 recites “controller adapted for obtaining quantitative information on average donor-acceptor distance or on average donor-acceptor distance changes in accordance with claim 1”.
Claim 15, line 5 recites “means for accommodating vessels”. Applicant’s specification does not give any examples of a means for accommodating vessels, and thus it is not clear as to what this limitation means. However, for examination purposes, the limitation is interpreted to encompass anything that can accommodate, i.e., hold, vessels (any kind of vessels).
Claim 15, line 12 recites “means for performing an eFRET measurement”.
Paragraph 0180 discloses a “detector” generically. It appears that Applicant intends to refer to known detectors for FRET, and therefore “ means for performing an eFRET measurement” is interpreted to refer to detectors for FRET known at the time of Applicant’s effective filing date.
Claim 15, line 14 recites “control means adapted for controlling the means for accommodating the vessel; controlling the at least one light source…..controlling the at least one light detector….and controlling said means for performing the eFRET measurement”. Applicant’s specification does not give an example of the recited “control means”, and thus it is not clear as to what this limitation means. For examination purposes, the limitation is interpreted to encompass anything (such as a computer and electronics) that can control the recited limitations.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim 1-18 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Claim 1 recites:
“A method for obtaining quantitative information on average donor-acceptor distance changes within a molecule using ensemble Forster resonance energy transfer (eFRET), the method comprising the steps of:
- obtaining a donor sample, wherein said donor sample comprising at least a donor and/or donor-labelled copies of said molecule;
- obtaining an acceptor sample comprising at least an acceptor and/or acceptor- labelled copies of said molecule; and
- obtaining at least a donor-acceptor-labelled sample comprising donor-acceptor- labelled copies of said molecule;
- performing an eFRET measurement for the donor-acceptor-labelled sample under a first condition and a second condition to obtain for this samples a first eFRET result under the first condition and a second eFRET result under the second condition, wherein the eFRET measurements of the donor-acceptor-labelled sample are performed using multiple respective molecule copies;
- performing at least an eFRET measurement for the donor sample under at least one condition to obtain for this sample a first eFRET result
and calculating a leakage coefficient (cik) from said donor sample;
- performing at least an eFRET measurement for the acceptor sample under at least one
condition to obtain for this sample a first eFRET result
and calculating a direct excitation coefficient (cdirE);
- correcting the donor-acceptor-labelled eFRET results based on the leakage coefficient (cik) and the direct excitation coefficient (cdirE);
wherein the first and/or the second eFRET results comprise respective measurement values of the
- emission of the acceptor after donor excitation (FDA(A)),
- emission of the acceptor after acceptor excitation (FAA(A)), and/or
- emission of the donor after donor excitation (FDD(D)),
- emission of the donor after acceptor excitation (FDA(D))
wherein said leackage coefficient (clk) is determined based on the ratio of FDA(D) and FDD(D); and said direct excitation coefficient (CdirE) is determined based on the ratio of FDA(A) and FAA(A);
- calculating a y-correction factor based on the donor-acceptor-labelled sample(s), ),wherein the y-correction factor is based on the negative ratio of i) the difference of FDA between the first and the second condition and ii) the difference of FDDof the donor-acceptor-labelled sample between the first and the second condition;
- determining condition-specific eFRET efficiencies based on the corrected donor- acceptor-labelled eFRET results and by using the y-correction factor; and
- determining quantitative information on average donor-acceptor distance changes within the molecule under the first and the second condition using the condition-specific eFRET efficiencies.” (Emphasis added).
The following steps of claim 1 supports that claim 1 is directed to an abstract idea:
calculating a leakage coefficient (cik) from said donor sample;
and calculating a direct excitation coefficient (cdirE);
- correcting the donor-acceptor-labelled eFRET results based on the leakage coefficient (cik) and the direct excitation coefficient (cdirE);
wherein said leackage coefficient (clk) is determined based on the ratio of FDA(D) and FDD(D); and said direct excitation coefficient (CdirE) is determined based on the ratio of FDA(A) and FAA(A);
- calculating a y-correction factor based on the donor-acceptor-labelled sample(s), ),wherein the y-correction factor is based on the negative ratio of i) the difference of FDA between the first and the second condition and ii) the difference of FDDof the donor-acceptor-labelled sample between the first and the second condition;
- determining condition-specific eFRET efficiencies based on the corrected donor- acceptor-labelled eFRET results and by using the y-correction factor; and
- determining quantitative information on average donor-acceptor distance changes within the molecule under the first and the second condition using the condition-specific eFRET efficiencies.” Emphasis added.
These above steps of calculating…, determining…, correcting…. are judicial exceptions since they are abstract ideas (i.e., they encompass mental steps and/or are directed to a natural law such as mathematical concepts and/or a natural correlation between the recited limitations.)
The combination of elements of claim 1 fails to integrate the judicial exceptions into a practical application for the following reasons.
Obtaining a donor sample and performing eFRET measurements are data gathering steps required to use the correlation, and as such, do not add a meaningful limitation to the method as they are insignificant extra-solution activity.
Examiner notes that the last three lines of claim 1 recites: “determining quantitative information on average donor-acceptor distance changes within the molecule under the first and the second condition using the condition-specific eFRET efficiencies” (emphasis added). This determining step is based upon natural correlations recited in claim 1 (as noted above). The recited calculation is an abstract idea (encompassing a mental step and/or a mathematical concept and/or a natural correlation), and the recited determination of quantitative information on average donor-acceptor distance changes within a molecule is also an abstract idea (i.e., a mental step and/or a natural correlation (between the quantitative information and the “condition-specific eFRET efficiencies” (last 2 lines of claim 1). Since such recited calculation and determination steps are themselves judicial exceptions (i.e., abstract ideas), they cannot be considered to amount to a specific practical application.
To elaborate, Examiner notes that “calculating a leakage coefficient from the donor sample (lines 16-17 of claim 1) is an abstract idea and data gathering.
Also, “correcting the donor-acceptor-labelled eFRET results based on the leakage coefficient (cik) and the direct excitation coefficient (cdirE)” (lines 21-22 of claim 1) is an abstract idea and/or encompasses a mental step.
Also, “determining condition-specific eFRET efficiencies based on the corrected donor- acceptor-labelled eFRET results and by using the y-correction factor” (lines 36-37 of claim 1) is an abstract idea and/or encompasses a mental step.
Moreover, “determining quantitative information on average donor-acceptor distance changes within the molecule under the first and the second condition using the condition-specific eFRET efficiencies” (the last 3 lines of claim 1) is an abstract idea since it encompasses a mental step and/or a natural correlation between the recited quantitative information and the condition-specific eFRET efficiencies.
For the above reasons, the combination of elements of claim 1 fails to integrate the judicial exceptions into a practical application. As noted above, the recited limitations are judicial exceptions themselves, or the limitations are data gathering steps required to use the judicial exceptions, and as such, cannot be considered a practical application of the judicial exceptions as they are extra-solution activity.
Also, claim 1 does not include additional elements that are sufficient to amount to significantly more than the judicial exception for the following reasons.
Performing an assay using eFRET (ensemble Forster resonance energy transfer) is a well-known assay that is conventional and routinely used in the assay art, as shown by US 20050048555 (hereinafter “Holmes”), and US 20070109536 (hereinafter “Weiss”), as discussed further below.
As a preliminary matter, while Applicant recites “ensemble Forster resonance energy transfer (eFRET)” in the preamble of claim 1, and also discloses “ensemble Förster Resonance Energy Transfer (eFRET; in the following also called quantumFRET)” (see para. 1 of US PreGrant Publication 20240044879), Examiner notes that ensemble Forster resonance energy transfer, or quantumFRET, appears to be the same as what is generally known as Forster resonance energy transfer (FRET). In other words, it does not appear that “ensemble Forster resonance energy transfer”, or “quantumFRET”, is any different from what is generally known in the art as Forster resonance energy transfer (FRET), which Examiner notes is well-known in the art, conventional, and routinely used in the assay art, as shown, for example, by Holmes (US 20050048555) and Weiss (US 20070109536), as discussed below.
Holmes (US 20050048555) (published in 2005) discloses the following.
“Although relatively new to imaging, the general idea of FRET has been used with spectroscopy instrumentation for many years in biochemistry. The two protein components being studied are labeled with separate fluorophores. A quantum FRET event occurs when one of the labeled protein components (the donor) absorbs an excitation photon, and, rather than emitting a fluorescent photon, it transfers the energy to the other labeled protein component (the acceptor). A percentage of these FRET events will then be converted to a fluorescence emission from the acceptor. Such FRET events occur only when the two protein components are within a few nanometers from each other, and must therefore be bound to each other or to a common macromolecule. In a simplistic sense, FRET is detected then, and in turn the protein-protein interaction detected, by utilizing an excitation filter tuned to the donor dye and an emission filter tuned to the acceptor dye.” Para. 0006 (emphasis added).
Thus FRET (or eFRET) has been used in the assay art for many years and is a well-known, routine, and conventional detection technique, as supported by the Holmes reference.
Weiss (published 2007) discloses the following.
“Single-molecule fluorescence spectroscopy (SMFS) is an ultra-sensitive optical method for detection and analysis of individual molecules. SMFS uses laser-excitation sources to probe individual diffusing or surface-immobilized fluorescent molecules and measure their fluorescence intensity, lifetime, anisotropy, and/or spectra, yielding information about molecular structure, interactions, and dynamics. During solution-based SMFS of dilute solutions of fluorescent species, single species are observed as fluorescence "bursts" that arise when the species diffuses through the detection volume. Often, the existence of an interaction is identified using Forster resonance energy transfer (FRET). If a molecule is labeled by a pair of complementary fluorescent probes (a donor, D; and an acceptor, A) in close proximity (2-10 nm), FRET can serve as a "molecular ruler", yielding D-A distance information. FRET has been used widely for analysis of: structure and dynamics of ensembles; single-molecules (kinetics of protein and RNA folding); DNA dynamics; rotation of molecular motors; heterogeneity/dynamics of protein-DNA complexes; and single cells (using naturally-fluorescent proteins, such as GFPs and dsRed).” Para. 0017 (emphasis added).
Thus FRET (or eFRET) has been widely used in the assay art and is a well-known, routine, and conventional detection technique, as supported by the Weiss reference.
In summary, the limitations of claim 1 relate to data gathering required to use the judicial exceptions identified further above, or are themselves judicial exceptions, as mentioned further above, neither of which can be considered a practical application or “significantly more” than the judicial exceptions. Moreover, eFRET is a well-known, routine and conventional assay technique and as such does not amount to significantly more than the identified judicial exceptions.
Regarding claim 2, this claim also recites steps of calculating…, determining…, and correcting…., which are judicial exceptions since they are abstract ideas (i.e., they encompass mental steps and/or are directed to a natural law such as mathematical concepts and/or a natural correlation between the recited limitations.) The combination of elements of claim 2 fails to integrate the judicial exceptions into a practical application and does not include additional elements that are sufficient to amount to significantly more than the judicial exception for the same reasons as set forth above regarding claim 1 for the same or similar, corresponding limitations.
Regarding claim 3, the steps of obtaining a first, second, and third sample…, and labelling molecule copies… relates to data gathering necessary to use the judicial exceptions noted in claim 1, and as such, do not add a meaningful limitation to the method as they are insignificant extra-solution activity. (They do not amount to a practical application or significantly more than the judicial exceptions.)
Regarding claim 4, the limitations of this claim recite properties of the donor and acceptor in the FRET system, which are still part of the FRET assay. Thus the limitations of claim 4 merely relate to the data gathering necessary to use the judicial exceptions noted above, and do not add meaningful limitation to the method and do not amount to significantly more than the judicial exceptions.
Regarding claim 5, the steps of transmitting light as recited are part of performing the FRET assay, and thus are part of the data gathering necessary to use the judicial exceptions, which do not add a meaningful limitation to the method, for the reasons set forth above.
Regarding claim 6, the limitations regarding the light illumination are part of performing the FRET assay, and thus are part of the data gathering necessary to use the judicial exceptions, which do not add a meaningful limitation to the method.
Regarding claim 7, the recited limitations relate to details that are merely part of a judicial exception, i.e., part of determining the leackage coefficient obtained for the donor sample (an abstract idea). Therefore claim 7 merely further recites the judicial exception, and as such, claim 7 does not recite any further limitations that can be considered a practical application of the judicial exception or limitations that are significantly more than the judicial exception.
Regarding claim 8, the limitations regarding the first and second condition of the eFRET measurement relate to data gathering necessary to use the judicial exceptions, and thus do not add a meaningful limitation to the method.
Regarding claim 9, the steps of “determining condition-specific correction factors….”,
and “correcting the first and second eFRET results…”
and “determining an inter-condition correction factor…”
and “correcting the condition-specific corrected first and second eFRET results…” as recited
are judicial exceptions since they are abstract ideas (i.e., they encompass mental steps and/or are directed to a natural law such as mathematical concepts and/or a natural correlation between the recited limitations.) The combination of elements of claim 9 fails to integrate the judicial exceptions into a practical application and does not include additional elements that are sufficient to amount to significantly more than the judicial exception (abstract idea) for similar reasons as set forth above regarding claim 1.
Regarding claims 10, 11, 12, and 13, the determining steps recited in these claims are abstract ideas for the same reasons as set forth above in claim 1. Moreover, there are no elements that integrate the judicial exceptions into a practical application nor that amount to significantly more than the judicial exceptions.
Regarding claim 14, obtaining information on a donor-acceptor specific Forster radius, and on a donor-acceptor distance as recited relates to data gathering necessary to use the judicial exceptions, which do not add a meaningful limitation to the method.
Regarding claim 15, which recites a system. Examiner notes that claim 15 recites a “measurement system comprising a controller adapted for obtaining quantitative information on average donor-acceptor distance or on average donor-acceptor distance changes in accordance with claim 1” (see first 3 lines of claim 15). Thus the claimed system is interpreted to include a controller for performing the method of claim 1. Moreover, Examiner notes that a controller is understood to encompass a computer (see for example paragraphs 0048 and 0173 of Applicant’s specification in US PreGrant Publication 20240044879). Thus the claim is directed to an abstract idea (obtaining quantitative information on average donor-acceptor distance or on average donor-acceptor distance changes in according with claim 1) with additional generic computer element (i.e., “controller”), but the generically recited computer element does not add a meaningful limitation to the abstract idea because the claim amounts to simply implementing the abstract idea on a generic computer. Moreover, a computer capable of performing FRET and calculations encompasses a well-known, routine, and conventional computer, and such is exemplified by Holmes (US 20050048555, see paragraph 0027).
Moreover, while claim 15 further recites structural limitations regarding the measurement system, including means for accommodating vessels, a light source, a light detector, means for performing an eFRET measurement, and control means, these limitations are well-known elements of a system for performing eFRET (i.e., FRET) measurements. These well-known elements for performing FRET are exemplified by Weiss (US 20070109536). See paragraph 0009 disclosing a microfluidic flow system and paragraph 0080 disclosing pipetting devices [the microfluidic flow system is equivalent to a means for accommodating vessels]. See paragraph 0100 disclosing CCD camera [a light detector] and laser [a light source]. See paragraph 0080 disclosing a measurement chamber [means for performing an eFRET measurement].
See also Holmes (US 20050048555) in paragraph 0027 disclosing a FRET processing system 10 for processing images 22 acquired from an image collection system 20 and generating a set of estimation images 24. Image collection system 20 may comprise, e.g., a fluorescence microscope and camera for collecting image data, as well as a computer system and/or database or memory for storing acquired image data. FRET processing system 10 includes: (1) a data input 17 for receiving image data; (2) a data output 19 for outputting estimation images 24; (3) an image alignment system 12 for aligning image data from acquired images 22 and/or 23; (4) an estimation system 14 that estimates the corrected FRET image, as well as donor and acceptor concentrations; and (5) an efficiency calculation system for calculating FRET efficiencies.
Thus, while claim 15 further recites structural limitations regarding the measurement system, including means for accommodating vessels, a light source, a light detector, means for performing an eFRET measurement, and control means, these limitations are well-known elements of a system for performing eFRET (i.e., FRET) measurements, such as exemplified by Weiss and Holmes.
Claim 16 recites use of a measurement system according to claim 15 to obtain quantitative information on average donor-acceptor distance changes within a molecule using ensemble Forster resonance energy transfer (eFRET) in accordance with a method comprising the steps recited in the body of claim 16. The discussion above regarding claims 1 and 15 are applicable to claim 16, which encompasses both.
Claim 17 recites a “computer program in combination with a measurement system according to claim 15, said computer program comprising instructions which, when the program is executed by a computer, cause the measurement system to carry out the method comprising” [the steps recited in the body of claim 17.] The discussion above regarding claims 1 and 15 are applicable to claim 17, which encompasses both. Moreover, utilizing a computer program to perform assays are well-known, routine, and conventional as shown by Holmes (US 20050048555) (see para. 0029 regarding computer hardware and software).
Claim 18 recites a “computer-readable data carrier comprising instructions which, when executed by a computer of measurement system according to claim 15, cause the computer and the measurement system to carry out the method comprising” [the steps recited in the body of claim 18]. The discussion above regarding claims 1 and 15 are applicable to claim 18, which encompasses both. Moreover, utilizing a computer-readable data carrier [software] to perform assays are well-known, routine, and conventional as shown by Holmes (US 20050048555) (see para. 0029 regarding computer hardware and software).
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
1) US 2005004855 (Holmes), while not teaching or suggesting the presently claimed limitations, discloses the following, generally known in FRET.
“FRET may also be used to measure the distance between two proteins or between two fluorophores that are bound to the same protein. This measurement relies on an equation involving a FRET efficiency calculated from a set of images. Today, most biologists who use FRET are interested in knowing: (1) whether or not FRET is happening at all, and (2), if so, where it is happening (i.e., where in the cell).” Para. 0008.
“The main limitations in existing FRET algorithms are due to two interrelated phenomena. (1) In order for FRET to occur, the emission spectrum of the donor fluorophore must overlap with the excitation spectrum of the acceptor fluorophore. Consequently the excitation and emission spectra of both dyes usually overlap and cross-talk and bleed-through are unavoidable. (2) As a result, the transfer equations that describe acquired images as functions of the desired FRET efficiency and other quantities do not have a closed-form solution. Accordingly, it is impossible to absolutely calculate a FRET image from a set of acquired images. Instead, existing algorithms rely on loosely justified approximations and assumptions to arrive at a solution. Para. 0009.
2) US 20070109536 (Weiss), while not teaching or suggesting the presently claimed invention, discloses that FRET has been used widely for analysis of structure and dynamics of ensemble (see paras. 0017-0019).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Ann Montgomery whose telephone number is (571)272-0894. The examiner can normally be reached Mon-Fri, 9-5:30 PM PST.
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/Ann Montgomery/Primary Examiner, Art Unit 1678