DETAILED ACTION
Notice of 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 .
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Withdrawal of Objections and Rejections
Applicant's response, filed 02/17/2026, has been fully considered.
In view of the amendment and remarks from 02/17/2026, the objection to the specification and the rejection of the following claims are withdrawn:
claims 11 and 13 under 35 USC § 112(b)
claims 1-3, 10, 12 and 14-16 under 35 U.S.C. 102.
The following rejections and/or objections are either maintained or newly applied for claims 1-16. They constitute the complete set applied to the instant application. Herein, "the previous Office action" refers to the Non-Final Rejection of 11/17/2025.
Status of the Claims
Claims 1-16 are pending.
Claims 1-16 are rejected.
Priority
This US Application 17/924,650 (11/10/2022) a 371 of PCT EP2021/061366 (04/30/2021) and claims priority from Foreign Application No. EP 20183910.7 (07/03/2020) and EP20174320.0 (05/13/2020), as reflected in the filing receipt mailed on 03/14/ 2023. The claims to the benefit of priority are acknowledged and the effective filing date of claims 1-16 is 05/13/2020.
Claim objections
Claim 11 is objected to because of the following informality: the recited "BBCH" should be spelled out completely. Appropriate correction is required.
Claim Interpretation
Claims 1, 5-9, 13 and 15-16 recites “if” statements which represent on contingent limitations (MPEP 2111.04.II) because the limitations only exist if a condition is met; causing the limitations to be non-requirements. See MPEP 2111.04 which states "If the claimed invention may be practiced without either the first or second condition happening, then neither step A or B is required by the broadest reasonable interpretation of the claim." If the Applicant intends for the contingent limitations to have patentable weight, then it is suggested to amend the claims to require their performance.
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 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 having 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) 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):
(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” or the generic placeholder) 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). The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) 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” or the generic placeholder) 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). The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) 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” or the generic placeholder) are being interpreted under 35 U.S.C. 112(f) except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word "means" (or "step” or the generic placeholder) are not being interpreted under 35 U.S.C. 112(f) except as otherwise indicated in an Office action.
Such claim limitations that use the term "control and calculation unit” being interpreted under 112(f) are:
the control and calculation unit is configured to compare, in a first phase, each transmitted sequence of a nucleic acid or a peptide with at least one pathogen sequence; and if the transmitted sequence does not match the at least one pathogen sequence, to prompt the sequencing unit to abort further sequencing of the respective nucleic acid or the respective peptide; if the transmitted sequence matches a pathogen sequence, to ascertain a pathogen having the pathogen sequence and to use the ascertained pathogen to ascertain at least one resistance marker, and to make a switch to a second phase; wherein the control and calculation unit is configured to compare, in the second phase, sequences of the nucleic acids or peptides in the sample with the at least one ascertained resistance marker and/or a resistance-free sequence (claim 15).
Because these claim limitations are being interpreted under 35 U.S.C. 112(f), they are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof. As it appears in the instant specification and claims, there is insufficient structure to describe the "control and calculation unit”. The specification must disclose structural components (computer/processor and algorithm) responsible for the performance of the claimed specific computer function, or else the claim is indefinite under 35 U.S.C. 112(b) (MPEP 2181 (II)(B)).
Claim 15 recites: the control and calculation unit is configured to compare, in a first phase, each transmitted sequence of a nucleic acid or a peptide with at least one pathogen sequence; and if the transmitted sequence does not match the at least one pathogen sequence, to prompt the sequencing unit to abort further sequencing of the respective nucleic acid or the respective peptide; if the transmitted sequence matches a pathogen sequence, to ascertain a pathogen having the pathogen sequence and to use the ascertained pathogen to ascertain at least one resistance marker, and to make a switch to a second phase; wherein the control and calculation unit is configured to compare, in the second phase, sequences of the nucleic acids or peptides in the sample with the at least one ascertained resistance marker and/or a resistance-free sequence. While the claim does recite algorithmic steps, it does not recite a processor or computer coupled to the unit so there is not sufficient structure recited in the claim; which justifies the interpretation.
If applicant does not intend to have this limitation interpreted under 35 U.S.C. 112(f), applicant may: (1) amend the claim limitations to avoid them being interpreted under 35 U.S.C. 112(f) (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitations recite sufficient structure to perform the claimed function so as to avoid them being interpreted under 35 U.S.C. 112(f).
Response to applicant's remarks in regard to 35 U.S.C. ~ 112(f)
The Remarks of 02/17/2026 have been fully considered but are not persuasive for the reasons below:
Applicant asserts in pg. 10 para. 4:
As is clear, the pending claims satisfy the requirement under Section 112(±) of providing adequate structure as performing the claimed function. Reconsideration and withdrawal of the present rejection are requested.
The Examiner would like to affirm that neither the previous office action or the instant examination describes any rejection associated with lack of adequate structure as performing the claimed function. The Claim Interpretation section was previously presented and maintained here due to fact that claim limitations in this application use the word "means" (or "step” or the generic placeholder); which requires interpretation under 35 U.S.C. 112(f). In this instant case, there are no rejections linked to the 112(f) Claim Interpretation due to the fact that adequate structure was identified for performing the claimed function.
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.
Claims 1-13 and 15-16 are rejected under 35 USC § 101 because the claimed inventions are directed to one or more Judicial Exceptions (JEs) without significantly more. Regarding JEs, "Claims directed to nothing more than abstract ideas..., natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 §I). Abstract ideas include mathematical concepts and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)).
101 background
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Analysis of instant claims
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The instant claims are directed to a method (claims 1-13), a system (claim 15), and a CRM (claim 16); each of which falls within one of the categories of statutory subject matter.
[Step 1: claims 1-13 and 15-16: Yes]
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Background
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
Analysis of instant claims
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and mathematical concepts (in particular mathematical relationships and formulas) as well as a law of nature or a natural phenomenon are as follows:
• "identifying signs of resistance of the pathogen to a control agent" (independent claim 1);
• "ascertaining environmental conditions to which the plant is exposed and/or has been exposed" (claims 2-4);
• "ascertaining at least one pathogen which can attack the plant" (claims 3-4);
• "ascertaining at least one pathogen sequence for the at least one ascertained pathogen" (claim 3);
• "ascertaining at least one resistance marker for the identified pathogen" (claims 3-4, 7, 9);
• "identifying signs of resistance of the identified pathogen to the control agent" (claims 3-4, 7);
• "calculating a probability of the at least one pathogen occurring currently for the plant" (claim 4);
• "comparing the probability with a predefined threshold value" (claim 4);
• "ascertaining pathogen sequences for those ascertained pathogens for which the probability is above the predefined threshold value" (claim 4);
• "comparing the sequences of the nucleic acids or peptides in the sample with the at least one ascertained resistance marker" (claims 5-6, 9);
• " ascertaining a resistance-free sequence for the identified pathogen" (claim 7 and 9);
• "ascertaining a target sequence for the identified pathogen" (claim 8);
• "identifying signs of a new resistance of the identified pathogen to the control agent by comparison of the sequences of nucleic acids or peptides in the sample with the target sequence" (claim 8);
• "ascertaining a frequency QR of nucleic acids or peptides found in the sample that have a sequence according to the resistance marker" (claim 9);
• "ascertaining a frequency QNR of nucleic acids or peptides found in the sample that have a sequence according to the resistance-free sequence" (claim 9);
• "calculating a ratio of the ascertained frequencies QR and QNR, and comparing the ratio with a predefined minimum value" (claim 9);
• "creating and/or updating a pathogen map, wherein a location is recorded in the pathogen map" (claim 13);
• "ascertain sequences of nucleotides or amino acids in the sample" (independent claim 15);
• "compare, in a first phase, each transmitted sequence of a nucleic acid or a peptide with at least one pathogen sequence" (independent claim 15);
• prompt the sequencing unit to abort further sequencing of the respective nucleic acid or the respective peptide" (independent claim 15);
• "ascertain a pathogen having the pathogen sequence and to use the ascertained pathogen to ascertain at least one resistance marker" (independent claim 15);
• "make a switch to a second phase; wherein the control and calculation unit is configured to compare, in the second phase, sequences of the nucleic acids or peptides in the sample with the at least one ascertained resistance marker and/or a resistance-free sequence" (independent claim 15);
• "checking whether the succession of nucleotides or amino acids is singly or multiply present in at least one pathogen sequence" (independent claim 16);
• "ascertaining at least one reference marker" (independent claim 16);
• "initiating a second phase; and in the second phase: comparing the successions of nucleotides or amino acids with the at least one reference marker and/or a resistance-free sequence, wherein the resistance-free sequence is a succession of nucleotides or a succession of amino acids of a pathogen that does not exhibit signs of resistance of the pathogen to the control agent" (independent claim 16).
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation. Without further detail as to the methodology involved in "calculating the probability of a pathogen occurring in a plant" based on "a ratio of the ascertained frequencies" and comparison to control, under the BRI, one may simply, for example, use pen and paper to perform mathematical steps to arrive at such probability and frequencies values. Further support for the mathematical techniques used in the claims is provided in the specification at pg. 10 line 25 (i.e. probability calculation) and pg. 16 lines 1-4 (i.e. calculation of ratios of frequencies). Under the BRI, the recited limitations are mental processes because a human mind is sufficiently capable of : identify a plant; identify a control agent such as a fungicide; identify if a plant disease resists the application of a control agent such a fungicide while considering a resistance occurrence; identify a pathogen that harms a plant; identify a pathogen sequence, a resistance free sequence and/or a pathogen marker given the data obtained after comparing sequencing data to a reference data; and identify environmental conditions that a plant is under.
[Step 2A Prong One: claims 1-13 and 15-16: Yes]
Step 2A, 1st prong, 1st Mayo/Alice question: natural product -- MPEP 2106.I and 2106.04
The instant claims recite a natural correlation by correlating the measurement of an amount of nucleotides and/or peptides found in nature with the existence of disease resistance. (see MPEP 2106.04(b).I).
[Step 2A Prong One: claims 1-13 and 15-16: Yes]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Background
MPEP 2106.04(d).I lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
Analysis of instant claims
Instant claims 1, 11-14, 16, and 23-26 recite additional elements that are not abstract ideas:
• "sequencing individual nucleic acids or individual peptides in the sample" (independent claims 1 and 15-16);
• "collecting the sample of the plant or of the medium in which the plant is growing" (claims 3-4, 7-9);
• "identifying the pathogen in the sample" (claims 1-4, 7-9);
• "outputting a notification indicating that a pathogen having a mutation pointing to a new and/or spreading resistance was identified in the sample" (claim 7);
• "outputting the pathogen map" (claim 13);
• "displaying the pathogen map on a screen" (claim 13);
• "outputting the pathogen map on a printer" (claim 13);
• "transmitting the pathogen map to a device for automatic execution of a measure to control the identified pathogen" (claim 13);
• "a sequencing unit; a control and calculation unit" (independent claim 15);
• "transmit, during the ascertainment of the sequences, the respectively ascertained sequences to the control and calculation unit" (independent claim 15);
• "computer" (independent claim 16); and
• "receiving a growing succession of nucleotides or amino acids in the respective nucleic acid or the respective peptide from a sequencing unit" (independent claim 16).
Dependent claim 10 further limits the plant sample to being a leaf or multiple leaves of the plant; dependent claim 11 further limits the plant sample to being in principal growth stage 1 or 2 or 3 to 6 according to a BBCH scale; and dependent claim 12 further the pathogen sequence ascertained to being a succession of DNA nucleotides from a fungus or bacterium or virus.
Considerations under Step 2A, Prong Two
The recited limitations in claims 7, 13 and 15-16 are interpreted as requiring the use of a computer. The use of a computer is broadly interpreted and not actually described in the claims or specification. Hence, the claims explicitly recite steps executed by computers and therefore can be described as computer functions or instructions to implement on a generic computer.
Further steps directed to additional non-abstract elements of a computing device/computer do not describe any specific computational steps by which the "computer parts" perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. The instant claims state nothing more than that a generic computer performs the functions that constitute the abstract idea (MPEP 2106.05(f)).
The recited claims "collecting the sample of the plant or of the medium in which the plant is growing" (claims 3-4, 7-9) read on data gathering activities; not amounting to a practical application. The type of data doesn’t change that it is mere data gathering.
Claims reciting “identifying a pathogen in the sample” (claims 1-4 and 7-9); and “sequencing individual nucleic acids or individual peptides in the sample” (claims 1 and 15-16); read on reads on detecting DNA in a sample, being an insignificant extra-solution activity since this limitation merely serve to gather data that is utilized as input for the judicial exception. See MPEP 2106.05(g) and MPEP 2106.04(d).
Claims reciting “outputting a notification” (claims 5-9); “outputting the pathogen map” (claim 13); “transmit/transmitting” (claims 13 and 15-16); “prompt the sequencing unit to abort further sequencing” (claim 15); “receiving a growing succession of nucleotides or amino acids in the respective nucleic acid or the respective peptide from a sequencing unit” (claim 16); read on receiving or transmitting data over a network, e.g., using the Internet to gather data, Symantec, 838 F.3d at 1321.
Claims reciting “sequencing unit” (claims 15-16); “control .. unit” (claim 15); “calculation unit” (claims 15); read on data gathering steps since the recited units are being used to gather data to be analyzed by the judicial exception.
There are no additional limitations to indicate details of exactly how the judicial exception is being integrated into a practical application. There are no additional limitations to indicate that the claimed computer, processor, or computer readable medium require anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. MPEP 2106.05(b).
Hence, these are mere instructions to apply the abstract idea using a computer and insignificant extra-solution activity and therefore the claims do not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; 2106.05(f); and 2106.05(g)). None of the dependent claims recite any additional non-abstract elements; they are all directed to further aspects of the information being analyzed, the manner in which that analysis is performed, or the mathematical operations performed on the information.
In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In this Step 2A, Prong Two immediately above claim steps and/or elements were identified as part of one or more additional elements. Additional elements are further discussed in Step 2B below.
Here in Step 2A, Prong Two, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
[Step 2A Prong Two: claims 1-13 and 15-16: No]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during examination that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
Claims 7, 13 and 15-16 recite a computer or computer functions, interpreted as instructions to apply the abstract idea using a computer, where the computer does not impose meaningful limitations on the judicial exceptions; which can be performed without the use of a computer (MPEP 2106.04(d) § I; and MPEP 2106.05(f)).
Further, the courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer when claimed in a generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versa ta Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(Il)(i)).
With respect to the instant claims, the prior art review to et. al. "High throughput sequencing for plant virus detection and discovery." Phytopathology 109(5):716-725 (2019); newly cited) discloses that the use “sequencing” assays on plant samples to identify pathogen resistance in plants are considered well-understood, routine and conventional in the art. Said portions of the prior art are, for example, pg. 719 Table 1.
When the claims are considered as a whole, they do not integrate the abstract idea into a practical application; they do not confine the use of the abstract idea to a particular technology; they do not solve a problem rooted in or arising from the use of a particular technology; they do not improve a technology by allowing the technology to perform a function that it previously was not capable of performing; and they do not provide any limitations beyond generally linking the use of the abstract idea to a broad technological environment. See MPEP 2106.05(a) and 2106.05(h).
The instant claims constitute insignificant extra solution activity, and when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(g)). Hence, these elements, when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(d)).
[Step 2B: claims 1-13 and 15-16: No]
Conclusion: Instant claims are directed to non-statutory subject matter
For the reasons above, the claims in this instant application, when the limitations are considered individually and as a whole, are directed to an abstract idea and lack an inventive concept not clearly anything significantly more.
Response to applicant's remarks in regard to Claim Rejection 35 U.S.C. ~ 101
The Remarks of 02/17/2026 have been fully considered but are not persuasive for the reasons below:
Applicant asserts in pg. 11 para. 5:
The claims not directed to the abstract idea of comparing sequences itself, but rather to a specific, improved method of sequencing that provides a tangible technical solution to technical problems identified in the art. As set forth in the Specification, prior art methods for detecting plant pathogens were limited. … The core of the technical improvement is the two-phase sequencing process recited in claim 1. … By aborting the sequencing of non-pathogen DNA in real-time, the claimed method prevents the sequencing apparatus from wasting time, computational resources, and reagents on irrelevant data. This is not "insignificant extra-solution activity;" it is an improvement to the data acquisition process itself, making it substantially more efficient and targeted. .. The combination of claim elements provides a specific, practical application that improves the functioning of sequencing technology. For at least these reasons, Applicant respectfully requests the withdrawal of the rejections under 35 U.S.C. § 101.
It appears that these remarks address Step 2A, Prong Two – 1st consideration regarding improvement over the previous state of a technology field (MPEP §§ 2106.04(d)(1) and 2106.05(a)). Regarding improvement to technology, the improvement cannot be in the judicial exception itself. Rather, the improvement is provided by the additional elements either on their own or in combination with the judicial exception. If the improvement is not realized in the additional elements then the improvement is in the judicial exception itself, which is not considered an improvement to technology. In this case, the sequencing step itself reads on data gathering activity and "aborting the sequencing of non-pathogen DNA in real-time" occurs if the ascertained sequence does not match the at least one pathogen sequence which is done due a comparing step; which is a mental process. Additionally, “if” statements represent contingent limitations (MPEP 2111.04.II) because the limitations only exist if a condition is met; causing the limitations to be non-requirements. See MPEP 2111.04.II which states "If the claimed invention may be practiced without either the first or second condition happening, then neither step A or B is required by the broadest reasonable interpretation of the claim."
Here, the claimed improvement is not realized by any additional element, as generic "sequencing" alone cannot integrate a judicial exception; as it is being identified as generic sequencing. If the Applicant intends for the contingent limitations to have patentable weight, then it is suggested to amend the claims to require their performance. In the case the claims actually affirmatively recite "aborting the sequencing based on the results", then there may be evidence for a practical application.
Applicant asserts in pg. 13 para. 1:
Furthermore, the claimed method, system, and CRM satisfy the transformation prong of the machine-or-transformation test, further confirming its patent eligibility. The process begins with a particular physical article-"a sample of a plant or of a medium in which the plant is growing" (Claim 1 )-which is a complex biological substance containing an uncharacterized mixture of nucleic acids and peptides from both the plant host and possible pathogens. This sample is subjected to a significant physical transformation by the claimed "sequencing" process. … This physical process transforms the raw, uncharacterized biological sample [the first article] into a different state or thing: a specific, curated set of digital sequence data representing the genetic identity of the pathogen and its resistance markers, culminating in a specific "notification" (Claims 5-9). … This transformation of a physical article into a different state or thing is precisely the type of activity that the machine-or-transformation test recognizes as patent-eligible. For these additional reasons, reconsideration and withdrawal of the present rejections under Section 101 are respectfully requested
It appears that these remarks address Step 2A, Prong Two – 4th consideration regarding 4. Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c). Regarding a transformation as a consideration for evaluating whether a judicial exception is integrated into a practical application, the transformation cannot be in the judicial exception itself. Rather, the transformation is provided by the additional elements either on their own or in combination with the judicial exception. In this case, transforming "the raw, uncharacterized biological sample [the first article] into a different state or thing: a specific, curated set of digital sequence data" does not qualify as a transformation provided by the additional elements either on their own or in combination with the judicial exception. In this case, the sequencing step itself reads on data gathering activity and "aborting the sequencing of non-pathogen DNA in real-time" occurs if the ascertained sequence does not match the at least one pathogen sequence which is done due a comparing step; which is a mental process. Claims directed to performing the identified judicial exceptions in a system and CRM are considered to perform the claimed abstract idea with a computer, which is not sufficient to integrate an abstract idea into a practical application (see MPEP 2106.05(f)); since steps that can be performed mentally and merely performing the mental process in a computer environment do not negate the fact that something that can be carried out in the human mind. See MPEP 2106.04(a)(2).III.C. MPEP 2106.05(c) states - For data, mere "manipulation of basic mathematical constructs the paradigmatic abstract idea, has not been deemed a transformation.”, - which indicates that transforming something physical into data isn’t a meaningful or particular transformation.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless -
(a)(l) the claimed invention was patented, described in a printed publication, or in public use, on sale,
or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
A. Claims 1-3, 10, 12 and 14-16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Capote (“Molecular Tools for Detection of Plant Pathogenic Fungi and Fungicide Resistance” Plant pathology 7:151-202 (2012)) as evidenced by Balzer ("Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim" Bioinformatics 26(18):i420-i425 (2010)), as cited on the attached Form PTO-892.
Claim 1 recites:
collecting a sample of a plant or of a medium in which the plant is growing: identifying a pathogen in the sample; identifying signs of resistance of the pathogen to a control agent; wherein the identification of the pathogen and the identification of the signs of resistance is done by sequencing individual nucleic acids or individual peptides in the sample, wherein sequences of nucleotides or sequences of amino acids are ascertained in the sequencing of the individual nucleic acids or individual peptides, wherein the sequences of nucleotides or sequences of amino acids are compared with reference sequences, wherein the sequencing is done in two phases, a first phase and a second phase; wherein, in the first phase, during the sequencing of each nucleic acid or each peptide, the respectively ascertained sequence is compared with at least one pathogen sequence.
• Capote teaches molecular tools for detection of plant pathogenic fungi and fungicide resistance (i.e. identifying the pathogen in a sample) (pg. 151 Title); wherein resistance to toxic compounds is a genetic adaptation of the fungus to one or more fungicides that leads to a reduction in sensitivity to these compounds (pg. 173 para. 4) and yield losses (pg. 152 para. 2) (i.e. identifying signs of resistance of the pathogen to a control agent); wherein roots, leaves, stems, flowers, fruits, seeds, soil, water or air are used as starting material and latent infections can be detected on symptomless plants (i.e. collecting a plant sample) (pg. 153 para. 2); wherein total DNA from the plant and the fungi can be isolated together from the infected plant tissue (pg. 153 para. 4); wherein molecular identification of plant pathogenic fungi is accomplished by PCR amplification of internal transcribed spacer region followed by either restriction analysis or direct sequencing (i.e. wherein the identification of the pathogen and the identification of the signs of resistance is done by sequencing individual nucleic acids or individual peptides in the sample, wherein sequences of nucleotides or sequences of amino acids are ascertained in the sequencing of the individual nucleic acids or individual peptides) and BLAST searching against GenBank or other databases (i.e. wherein the sequences of nucleotides or sequences of amino acids are compared with reference sequences) (pg. 155 para. 3); wherein fungal sequences in publicly accessible sequence databases, and sequences of selected genes (i.e. markers) have been widely used for the identification of specific pathogens (i.e. wherein the sequencing is done in two phases, a first phase and a second phase; wherein, in the first phase, during the sequencing of each nucleic acid or each peptide, the respectively ascertained sequence is compared with at least one pathogen sequence) (pg. 171 para. 3); wherein polymorphisms detected in the microsatellite flanking regions of Phytophthora infestans fungi allowed the development of a single nucleotide polymorphism genetic marker system for typing this pathogen (i.e. sequences of the nucleic acids or peptides in the sample are compared with the at least one ascertained resistance marker) (pg. 157 para. 1); wherein a DNA array for simultaneous detection of over 40 different plant pathogenic soilborne fungi and 10 bacteria that frequently occur in greenhouse crops (i.e. ascertaining the plant and ascertaining at least one pathogen which can attack the plant) (pg. 171 para. 2); wherein fungi resistance in plants depends on how resistance characters are inherited, the epidemiology of the fungus, the environment, and the persistence of selective pressure (i.e. ascertaining environmental conditions to which the plant is exposed and/or has been exposed and identifying resistance and resistance free cases) (pg. 174 para. 4).
if the ascertained sequence does not match the at least one pathogen sequence, further sequencing of said nucleic acid or said peptide is aborted; if the ascertained sequence matches the at least one pathogen sequence, a pathogen having the pathogen sequence is ascertained and the ascertained pathogen is used to ascertain at least one resistance marker, and a switch is made to the second phase; wherein, in the second phase, sequences of the nucleic acids or peptides in the sample are compared with the at least one ascertained resistance marker and/or with a resistance-free sequence, wherein a resistance-free sequence is a succession of nucleotides or a succession of amino acids of the pathogen that does not exhibit signs of resistance of the pathogen to the control agent
• Capote teaches primers designed to detect and identify Verticillium dahliae and V. alboatrum and to distinguish pathogenic and non-pathogenic Fusarium oxysporum in tomato (i.e. matching pathogenic and non-pathogenic sequences – first phase – where the non-pathogenic sequences reads on comparisons yielding a non-match) (pg. 156 para. 2); wherein the use of PCR amplification of a target gene with universal primers is followed by sequencing and comparison with the available publicly databases (i.e. reading on the second phase – sequencing comparison)( (pg. 171 para. 3);
• Capote does not teach "if the ascertained sequence does not match the at least one pathogen sequence, further sequencing of said nucleic acid or said peptide is aborted." However, teach high-throughput sequencing pipelines and analysis of data for virus detection that applies trimming low quality reads (i.e. sequences that are not desirable based on a chosen criteria) (pg. 719 col. 1 para. 3); wherein sequencing steps – i.e. sequences assembled into contigs - does not continue for sequences that are trimmed out (i.e. aborting sequencing steps for sequences that do not meet a criteria) (pg. 719 col;. 2 para. 1).
Claim 2 recites:
ascertaining the plant; ascertaining at least one pathogen which can attack the plant; ascertaining at least one pathogen sequence for the at least one ascertained pathogen; collecting the sample of the plant or of the medium in which the plant is growing; identifying the pathogen in the sample; ascertaining at least one resistance marker for the identified pathogen; and identifying signs of resistance of the identified pathogen to the control agent
• Capote teaches molecular tools for detection of plant pathogenic fungi and fungicide resistance (i.e. identifying the pathogen in a sample) (pg. 151 Title); wherein resistance to toxic compounds is a genetic adaptation of the fungus to one or more fungicides that leads to a reduction in sensitivity to these compounds (pg. 173 para. 4) and yield losses (pg. 152 para. 2) (i.e. identifying signs of resistance of the pathogen to a control agent); wherein roots, leaves, stems, flowers, fruits, seeds, soil, water or air are used as starting material and latent infections can be detected on symptomless plants (i.e. collecting a plant sample) (pg. 153 para. 2); wherein total DNA from the plant and the fungi can be isolated together from the infected plant tissue (pg. 153 para. 4); wherein molecular identification of plant pathogenic fungi is accomplished by PCR amplification of internal transcribed spacer region followed by either restriction analysis or direct sequencing (i.e. wherein the identification of the pathogen and the identification of the signs of resistance is done by sequencing individual nucleic acids or individual peptides in the sample, wherein sequences of nucleotides or sequences of amino acids are ascertained in the sequencing of the individual nucleic acids or individual peptides) and BLAST searching against GenBank or other databases (i.e. wherein the sequences of nucleotides or sequences of amino acids are compared with reference sequences) (pg. 155 para. 3).
Claim 3 recites:
ascertaining the plant; ascertaining environmental conditions to which the plant is exposed and/or has been exposed; ascertaining at least one pathogen which can attack the plant; ascertaining at least one pathogen sequence for the at least one ascertained pathogen; collecting the sample of the plant or of the medium in which the plant is growing; identifying the pathogen in the sample; ascertaining at least one resistance marker for the identified pathogen; and identifying signs of resistance of the identified pathogen to the control agent
• Capote teaches molecular tools for detection of plant pathogenic fungi and fungicide resistance (i.e. identifying the pathogen in a sample) (pg. 151 Title); wherein resistance to toxic compounds is a genetic adaptation of the fungus to one or more fungicides that leads to a reduction in sensitivity to these compounds (pg. 173 para. 4) and yield losses (pg. 152 para. 2) (i.e. identifying signs of resistance of the pathogen to a control agent); wherein roots, leaves, stems, flowers, fruits, seeds, soil, water or air are used as starting material and latent infections can be detected on symptomless plants (i.e. collecting a plant sample) (pg. 153 para. 2); wherein total DNA from the plant and the fungi can be isolated together from the infected plant tissue (pg. 153 para. 4); wherein molecular identification of plant pathogenic fungi is accomplished by PCR amplification of internal transcribed spacer region followed by either restriction analysis or direct sequencing (i.e. wherein the identification of the pathogen and the identification of the signs of resistance is done by sequencing individual nucleic acids or individual peptides in the sample, wherein sequences of nucleotides or sequences of amino acids are ascertained in the sequencing of the individual nucleic acids or individual peptides) and BLAST searching against GenBank or other databases (i.e. wherein the sequences of nucleotides or sequences of amino acids are compared with reference sequences) (pg. 155 para. 3); wherein a DNA array for simultaneous detection of over 40 different plant pathogenic soilborne fungi and 10 bacteria that frequently occur in greenhouse crops (i.e. ascertaining the plant and ascertaining at least one pathogen which can attack the plant) (pg. 171 para. 2); wherein fungi resistance in plants depends on how resistance characters are inherited, the epidemiology of the fungus, the environment, and the persistence of selective pressure (i.e. ascertaining environmental conditions to which the plant is exposed and/or has been exposed) (pg. 174 para. 4).
Claim 10 recites:
wherein the sample of the plant is a leaf or multiple leaves of the plant
• Capote teaches molecular tools for detection of plant pathogenic fungi and fungicide resistance (i.e. identifying the pathogen in a sample) (pg. 151 Title); wherein resistance to toxic compounds is a genetic adaptation of the fungus to one or more fungicides that leads to a reduction in sensitivity to these compounds (pg. 173 para. 4) and yield losses (pg. 152 para. 2) (i.e. identifying signs of resistance of the pathogen to a control agent); wherein roots, leaves, stems, flowers, fruits, seeds, soil, water or air are used as starting material and latent infections can be detected on symptomless plants (i.e. collecting a plant sample) (pg. 153 para. 2).
Claim 12 recites:
wherein the pathogen sequence is a succession of DNA nucleotides from a fungus or bacterium or virus.
• Capote teaches the molecular identification of plant pathogenic fungi is accomplished by PCR amplification of internal transcribed spacer region followed by either restriction analysis or direct sequencing and BLAST searching against GenBank or other databases (pg. 155 para. 3); wherein total DNA from the plant and the fungi can be isolated together from the infected plant tissue (pg. 153 para. 4).
Claim 14 recites:
ascertaining a control agent for controlling the identified pathogen, taking into account the resistance that may have been identified; and carrying out a measure to control the pathogen in the plant using the ascertained control agent
• Capote teaches the use of synthetic fungicides as a main strategy to control plant diseases (i.e. carrying out a measure to control the pathogen in the plant using the ascertained control agent); wherein the development of resistance to fungicides in fungal pathogens have resulted in a significant interest in knowing more about fungal resistance (i.e. taking into account the resistance that may have been identified) (pg. 152 para. 2).
Claim 15 recites:
a sequencing unit; a control and calculation unit; and at least one data store in which at least one pathogen sequence and at least one resistance marker are stored for at least one pathogen; wherein the sequencing unit is configured to sequence nucleic acids or peptides in a sample of a plant or of a medium in which the plant is growing and to thereby ascertain sequences of nucleotides or amino acids in the sample; wherein the sequencing unit is configured to transmit, during the ascertainment of the sequences, the respectively ascertained sequences to the control and calculation unit; wherein the control and calculation unit is configured to compare, in a first phase, each transmitted sequence of a nucleic acid or a peptide with at least one pathogen sequence; and if the transmitted sequence does not match the at least one pathogen sequence, to prompt the sequencing unit to abort further sequencing of the respective nucleic acid or the respective peptide; if the transmitted sequence matches a pathogen sequence, to ascertain a pathogen having the pathogen sequence and to use the ascertained pathogen to ascertain at least one resistance marker, and to make a switch to a second phase; wherein the control and calculation unit is configured to compare, in the second phase, sequences of the nucleic acids or peptides in the sample with the at least one ascertained resistance marker and/or a resistance-free sequence, wherein the resistance-free sequence is a succession of nucleotides or a succession of amino acids of a pathogen that does not exhibit signs of a resistance of the pathogen to the control agent
Claim 16 recites:
for a multiplicity of nucleic acids or peptides: receiving a growing succession of nucleotides or amino acids in the respective nucleic acid or the respective peptide from a sequencing unit; in a first phase while the growing succession is being received: checking whether the succession of nucleotides or amino acids is singly or multiply present in at least one pathogen sequence; wherein if the succession is not present in any pathogen sequence then transmitting a signal to the sequencing unit to abort further sequencing of the nucleic acid or the peptide; wherein if the succession matches a pathogen sequence then ascertaining a pathogen having the pathogen sequence, and ascertaining at least one reference marker, and initiating a second phase; and in the second phase: comparing the successions of nucleotides or amino acids with the at least one reference marker and/or a resistance-free sequence, wherein the resistance-free sequence is a succession of nucleotides or a succession of amino acids of a pathogen that does not exhibit signs of resistance of the pathogen to the control agent
• Capote teaches molecular tools for detection of plant pathogenic fungi and fungicide resistance (i.e. identifying the pathogen in a sample) (pg. 151 Title); wherein resistance to toxic compounds is a genetic adaptation of the fungus to one or more fungicides that leads to a reduction in sensitivity to these compounds (pg. 173 para. 4) and yield losses (pg. 152 para. 2); wherein total DNA from the plant and the fungi can be isolated together from the infected plant tissue (pg. 153 para. 4); wherein molecular identification of plant pathogenic fungi is accomplished by PCR amplification of internal transcribed spacer region followed by either restriction analysis or direct sequencing and BLAST searching against GenBank or other databases (i.e. wherein the sequences of nucleotides or sequences of amino acids are compared with reference sequences) (pg. 155 para. 3); wherein fungal sequences in publicly accessible sequence databases, and sequences of selected genes (i.e. markers) have been widely used for the identification of specific pathogens (i.e. wherein the sequencing is done in two phases, a first phase and a second phase; wherein, in the first phase, during the sequencing of each nucleic acid or each peptide, the respectively ascertained sequence is compared with at least one pathogen sequence) (pg. 171 para. 3); wherein polymorphisms detected in the microsatellite flanking regions of Phytophthora infestans fungi allowed the development of a single nucleotide polymorphism genetic marker system for typing this pathogen (i.e. sequences of the nucleic acids or peptides in the sample are compared with the at least one ascertained resistance marker) (pg. 157 para. 1); wherein a DNA array for simultaneous detection of over 40 different plant pathogenic soilborne fungi and 10 bacteria that frequently occur in greenhouse crops (i.e. ascertaining the plant and ascertaining at least one pathogen which can attack the plant) (pg. 171 para. 2); wherein fungi resistance in plants depends on how resistance characters are inherited, the epidemiology of the fungus, the environment, and the persistence of selective pressure (i.e. ascertaining environmental conditions to which the plant is exposed and/or has been exposed and identifying resistance/non-resistance) (pg. 174 para. 4); wherein primers are designed to detect and identify Verticillium dahliae and V. alboatrum and to distinguish pathogenic and non-pathogenic Fusarium oxysporum in tomato (i.e. matching pathogenic and non-pathogenic sequences – first phase – where the non-pathogenic sequences reads on comparisons yielding a non-match) (pg. 156 para. 2); wherein the use of PCR amplification of a target gene with universal primers is followed by sequencing and comparison with the available publicly databases (i.e. second phase – sequencing comparison)( (pg. 171 para. 3); wherein next-generation sequencing technologies commercially available are used for detection of plant pathogenic fungi and fungicide resistance include the 454 GS20 pyrosequencing-based instruments (Roche Applied Science), the Solexa 1G analyzer (Illumina, Inc.), and the SOLiD instrument (Applied Biosystems) (pg. 171 para. 4) (i.e. reading on sequencing units as evidence by Balzer pg. i420 col. 2 para. 2 configured to receive a growing succession of nucleotides and sequence nucleic acids identifying while data is being received the presence of single or multiple nucleotides including resistance markers, control units as evidence by Balzer pg. i423 col. 2 para. 4; configured to compare sequences as evidenced by Balzer pg. i422 col. 1 para. 3; and transmit information identified as evidenced by Balzer pg. i420 col. 2 para. 4; calculation units to analyze data sequenced as evidenced by Balzer pg.i422 col. 2 para. 3. The technologies taught by Capote inherently possess the architecture of a sequencing unit; a control and calculation unit with data and storage capacity configured to receive a growing sequence calculate values and compare it to a pathogen database as in claims 15 and 16; which is evidenced by the prior art to Blazer.
Claim Rejections - 35 USC § 103
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
B. Claims 4 and 13 are rejected under 35 U.S.C. 103(a) as being unpatentable over Capote as applied to claim 1 on the 102 rejection above further in view of Meentemeyer ("Early detection of emerging forest disease using dispersal estimation and ecological niche modeling." Ecological Applications 18(2):377-390 (2008)), as cited on the 11/17/25 Form PTO-892. Any newly recited portions are necessitated by claim amendment.
Claim 4 recites:
ascertaining the plant; ascertaining at least one pathogen which can attack the plant; ascertaining environmental conditions to which the plant is exposed or has been exposed; calculating a probability of the at least one pathogen occurring currently for the plant; comparing the probability with a predefined threshold value; ascertaining pathogen sequences for those ascertained pathogens for which the probability is above the predefined threshold value; collecting the sample of the plant or of the medium in which the plant is growing; identifying the pathogen in the sample; ascertaining at least one resistance marker for the identified pathogen; and identifying signs of resistance of the identified pathogen to the control agent
• Capote teaches molecular tools for detection of plant pathogenic fungi and fungicide resistance (i.e. identifying the pathogen in a sample) (pg. 151 Title); wherein resistance to toxic compounds is a genetic adaptation of the fungus to one or more fungicides that leads to a reduction in sensitivity to these compounds (pg. 173 para. 4) and yield losses (pg. 152 para. 2) (i.e. identifying signs of resistance of the pathogen to a control agent); wherein roots, leaves, stems, flowers, fruits, seeds, soil, water or air are used as starting material and latent infections can be detected on symptomless plants (i.e. collecting a plant sample) (pg. 153 para. 2); wherein total DNA from the plant and the fungi can be isolated together from the infected plant tissue (pg. 153 para. 4); wherein molecular identification of plant pathogenic fungi is accomplished by PCR amplification of internal transcribed spacer region followed by either restriction analysis or direct sequencing (pg. 171 para. 3); wherein polymorphisms detected in the microsatellite flanking regions of Phytophthora infestans fungus allowed the development of a single nucleotide polymorphism genetic marker system for typing this pathogen (i.e. ascertaining at least one resistance marker for the identified pathogen) (pg. 157 para. 1); wherein a DNA array for simultaneous detection of over 40 different plant pathogenic soilborne fungi and 10 bacteria that frequently occur in greenhouse crops (i.e. ascertaining the plant and ascertaining at least one pathogen which can attack the plant) (pg. 171 para. 2); wherein fungi resistance in plants depends on how resistance characters are inherited, the epidemiology of the fungus, the environment, and the persistence of selective pressure (i.e. ascertaining environmental conditions to which the plant is exposed and/or has been exposed) (pg. 174 para. 4).
• Capote does not teach “calculating a probability of the at least one pathogen occurring currently for the plant; comparing the probability with a predefined threshold value; ascertaining pathogen sequences for those ascertained pathogens for which the probability is above the predefined threshold value”. However, Meentemeyer teaches a method for early detection of Phytophthora ramorum disease outbreak using invasion probability models (pg. 377 para. 1); wherein the optimal threshold probability above which a plot should be considered infected was calculated using receiver operating characteristic analyses (i.e. calculating a probability of the at least one pathogen occurring currently for the plant; comparing the probability with a predefined threshold value) (pg. 383 col. 1 para. 2); wherein pathogen presence was confirmed through sequencing the internal transcribed spacer region of the nuclear ribosomal DNA and comparing with voucher sequences of P. ramorum (i.e. ascertaining pathogen sequences for those ascertained pathogens for which the probability is above the predefined threshold value) (pg. 380 col. 1 para. 2).
Claim 13 recites:
creating and/or updating a pathogen map, wherein a location is recorded in the pathogen map; wherein the sample of the plant has been collected at the location, wherein an indication is given for the location as to whether a pathogen has been identified in the plant and, if a pathogen has been identified in the plant, whether the pathogen has resistance to the control agent; and outputting the pathogen map, displaying the pathogen map on a screen and/or outputting the pathogen map on a printer and/or transmitting the pathogen map to a device for automatic execution of a measure to control the identified pathogen
• Capote does not teach the recitation above. However, Meentemeyer teaches a method for early detection of Phytophthora ramorum disease outbreak using dispersal models in a geographic information system predicted the presence of the pathogen (i.e. an indication is given for the location as to whether a pathogen has been identified in the plant) (pg. 377 para. 1); wherein niche and dispersal parameters were used to predict the locations of new infections, with accuracies ranging from 0.86 to 0.90 (pg. 377 para. 1); wherein habitat and spatial position variables are digitally mapped (i.e. wherein a location is recorded in the pathogen map) serving for guiding management with resulting model equations being applied and visualized in a geographic information system (i.e. displaying on a screen) (pg. 378 col. 1 para. 2); wherein new detections discovered through our sampling were also continually added to this data set (i.e. updating the pathogen database/map) (pg. 381 col. 2 para. 1).
Rationale for combining (MPEP §2142-2143)
Regarding claims 4 and 13, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Capote in view of Meentemeyer because all references disclose methods for the identification of pathogens in plants. The motivation would have been to incorporate software packages organized to incorporate probabilistic modeling to analyze the relative roles of niche and dispersal limitation in controlling the distribution of invasive pathogens (pg. 377 para. 1 Meentemeyer).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the method for the identification of pathogens in plants of Capote to the methods by Meentemeyer because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for identification of pathogens in plants.
C. Claims 5 and 8 are rejected under 35 U.S.C. 103(a) as being unpatentable over Capote as applied to claim 1 on the 102 rejection above further in view of Luvisi (“Electronic identification-based Web 2.0 application for plant pathology purposes” Computers and Electronics in Agriculture 84:7–15 (2012)), as cited on the 11/17/25 Form PTO-892. Any newly recited portions are necessitated by claim amendment.
Claim 5 recites:
wherein the step of identifying signs of resistance of the identified pathogen to the control agent comprises the following steps: comparing the sequences of the nucleic acids or peptides in the sample with the at least one ascertained resistance marker; wherein if the resistance marker does not occur in any of the sequences of the nucleic acids or peptides in the sample then outputting a notification indicating that no sign of resistance was found for the identified pathogen; and wherein if the resistance marker occurs in one or more of the sequences then outputting a notification indicating that a sign of resistance was found for the identified pathogen, and outputting a notification about the resistance
• Capote teaches that molecular identification of plant pathogenic fungi is accomplished by PCR amplification of internal transcribed spacer region followed by either restriction analysis or direct sequencing (i.e. ascertaining a target sequence for the identified pathogen) and BLAST searching against GenBank or other databases (i.e. identifying signs of a new resistance of the identified pathogen to the control agent by comparison of the sequences of nucleic acids or peptides in the sample with the target sequence) (pg. 155 para. 3); wherein fungal sequences in publicly accessible sequence databases, and sequences of selected genes (i.e. markers) have been widely used for the identification of specific pathogens (pg. 171 para. 3); wherein polymorphisms detected in the microsatellite flanking regions of Phytophthora infestans fungi allowed the development of a single nucleotide polymorphism genetic marker system for typing this pathogen (i.e. comparing the sequences of the nucleic acids or peptides in the sample with the at least one ascertained resistance marker) (pg. 157 para. 1); wherein primers are designed to detect and identify Verticillium dahliae and V. alboatrum and to distinguish pathogenic and non-pathogenic Fusarium oxysporum in tomato (i.e. matching pathogenic and non-pathogenic sequences – first phase – where the non-pathogenic sequences reads on comparisons yielding a non-match) (pg. 156 para. 2); wherein the use of PCR amplification of a target gene with universal primers is followed by sequencing and comparison with the available publicly databases (i.e. reading on the second phase – sequencing comparison)( (pg. 171 para. 3).
• Capote does not teach “wherein if the resistance marker does not occur in any of the sequences of the nucleic acids or peptides in the sample then outputting a notification indicating that no sign of resistance was found for the identified pathogen; and wherein if the resistance marker occurs in one or more of the sequences then outputting a notification indicating that a sign of resistance was found for the identified pathogen, and outputting a notification about the resistance.” However, Luvisi teaches electronic identification web-based tools in plant pathology for storing, updating and sharing information (pg. 7 para. 1); wherein the assay activity diagram shows a step where detailed results for assay setup by the user is shared to all users and laboratories (i.e. notification outputted could comprise any type of information the user desires) in both cases where the sample has a positive identification or negative identification for the pathogen (pg. 12 Fig. 3 and pg. 13 col. 1 para. 3).
Regarding “identifying signs of a new resistance”; a motivation to use the same steps already taught to find a new resistance originates from the “obvious to optimize” 2144.05 rationale ,which states that choosing from a finite number of identified, predictable solutions (i.e., in this case a finite number of steps already established to identify a plant pathogen/resistance), with a reasonable expectation of success would motivate one of ordinary skill in the art. See MPEP 2143 (I). Also see MPEP 2144.05 (a change in form, proportions, or degree "will not sustain a patent"); In re Williams, 36 F.2d 436, 438, 4 USPQ 237 (CCPA 1929) ("It is a settled principle of law that a mere carrying forward of an original patented conception involving only change of form, proportions, or degree, or the substitution of equivalents doing the same thing as the original invention, by substantially the same means, is not such an invention as will sustain a patent, even though the changes of the kind may produce better results than prior inventions."). See also KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416, 82 USPQ2d 1385, 1395 (2007) (identifying "the need for caution in granting a patent based on the combination of elements found in the prior art").
Claim 8 recites:
collecting the sample of the plant or of the medium in which the plant is growing; identifying the pathogen in the sample; ascertaining a target sequence for the identified pathogen; and identifying signs of a new resistance of the identified pathogen to the control agent by comparison of the sequences of nucleic acids or peptides in the sample with the target sequence; wherein if a sequence or a number of sequences that is greater than or equal to a minimum number represents a mutation of the target sequence then outputting a notification indicating that a pathogen having a mutation pointing to a new and/or spreading resistance was identified in the sample
• Capote teaches that molecular identification of plant pathogenic fungi is accomplished by PCR amplification of internal transcribed spacer region followed by either restriction analysis or direct sequencing (i.e. ascertaining a target sequence for the identified pathogen) and BLAST searching against GenBank or other databases (i.e. identifying signs of a new resistance of the identified pathogen to the control agent by comparison of the sequences of nucleic acids or peptides in the sample with the target sequence) (pg. 155 para. 3); wherein fungal sequences in publicly accessible sequence databases, and sequences of selected genes (i.e. markers) have been widely used for the identification of specific pathogens (pg. 171 para. 3); wherein polymorphisms detected in the microsatellite flanking regions of Phytophthora infestans fungi allowed the development of a single nucleotide polymorphism genetic marker system for typing this pathogen (i.e. comparing the sequences of the nucleic acids or peptides in the sample with the at least one ascertained resistance marker) (pg. 157 para. 1); wherein primers are designed to detect and identify Verticillium dahliae and V. alboatrum and to distinguish pathogenic and non-pathogenic Fusarium oxysporum in tomato (i.e. matching pathogenic and non-pathogenic sequences – first phase – where the non-pathogenic sequences reads on comparisons yielding a non-match) (pg. 156 para. 2); wherein the use of PCR amplification of a target gene with universal primers is followed by sequencing and comparison with the available publicly databases (i.e. reading on the second phase – sequencing comparison)( (pg. 171 para. 3).
• Capote does not teach “wherein if a sequence or a number of sequences that is greater than or equal to a minimum number represents a mutation of the target sequence then outputting a notification indicating that a pathogen having a mutation pointing to a new and/or spreading resistance was identified in the sample.” However, Luvisi teaches electronic identification web-based tools in plant pathology for storing, updating and sharing information (pg. 7 para. 1); wherein the assay activity diagram shows a step where detailed results for assay setup by the user is shared to all users and laboratories (i.e. notification outputted could comprise any type of information the user desires) in both cases where the sample has a positive identification or negative identification for the pathogen (pg. 12 Fig. 3 and pg. 13 col. 1 para. 3); wherein the method allows lab systems to move from isolated data stations toward more effective and integrated laboratory automation (pg. 15 col. 1 para. 3).
Regarding “identifying signs of a new resistance”; a motivation to use the same steps already taught to find a new resistance originates from the “obvious to optimize” 2144.05 rationale ,which states that choosing from a finite number of identified, predictable solutions (i.e., in this case a finite number of steps already established to identify a plant pathogen/resistance), with a reasonable expectation of success would motivate one of ordinary skill in the art. See MPEP 2143 (I). Also see MPEP 2144.05 (a change in form, proportions, or degree "will not sustain a patent"); In re Williams, 36 F.2d 436, 438, 4 USPQ 237 (CCPA 1929) ("It is a settled principle of law that a mere carrying forward of an original patented conception involving only change of form, proportions, or degree, or the substitution of equivalents doing the same thing as the original invention, by substantially the same means, is not such an invention as will sustain a patent, even though the changes of the kind may produce better results than prior inventions."). See also KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416, 82 USPQ2d 1385, 1395 (2007) (identifying "the need for caution in granting a patent based on the combination of elements found in the prior art").
Rationale for combining (MPEP §2142-2143)
Regarding claims 5 and 8, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Capote in view of Luvisi because all references disclose methods for investigating pathogen detection in plants. The motivation would have been to support research data management and interaction between users in the detection of pathogen in plants (pg. 7 para. 1 Luvisi).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the method for the investigating pathogen detection of Capote to the methods by Luvisi because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for investigating pathogen detection in plants.
D. Claims 6-7 are rejected under 35 U.S.C. 103(a) as being unpatentable over Capote as applied to claim 1 on the 102 rejection further in view of Luvisi and Meyers ("Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide‐binding superfamily." The Plant Journal 20(3):317-332 (1999)), as cited on the 11/17/25 Form PTO-892. Any newly recited portions are necessitated by claim amendment.
Claim 6 recites:
comparing the sequences of the nucleic acids or peptides in the sample with the at least one ascertained resistance marker; wherein if the resistance marker does not occur in any of the sequences of the nucleic acids or peptides in the sample or occurs in a number of nucleic acids that is smaller than a predefined minimum number then outputting a notification indicating that no sign of a resistance was found for the identified pathogen; wherein if the resistance marker occurs in a minimum number of sequences or in a number greater than the predefined minimum number then outputting a notification indicating that a sign of resistance was found for the identified pathogen, and outputting a notification about the resistance
• Capote teaches that molecular identification of plant pathogenic fungi is accomplished by PCR amplification of internal transcribed spacer region followed by either restriction analysis or direct sequencing (i.e. ascertaining a target sequence for the identified pathogen) and BLAST searching against GenBank or other databases (i.e. identifying signs of a new resistance of the identified pathogen to the control agent by comparison of the sequences of nucleic acids or peptides in the sample with the target sequence) (pg. 155 para. 3); wherein fungal sequences in publicly accessible sequence databases, and sequences of selected genes (i.e. markers) have been widely used for the identification of specific pathogens (pg. 171 para. 3); wherein polymorphisms detected in the microsatellite flanking regions of Phytophthora infestans fungi allowed the development of a single nucleotide polymorphism genetic marker system for typing this pathogen (i.e. comparing the sequences of the nucleic acids or peptides in the sample with the at least one ascertained resistance marker) (pg. 157 para. 1); wherein primers are designed to detect and identify Verticillium dahliae and V. alboatrum and to distinguish pathogenic and non-pathogenic Fusarium oxysporum in tomato (i.e. matching pathogenic and non-pathogenic sequences – first phase – where the non-pathogenic sequences reads on comparisons yielding a non-match) (pg. 156 para. 2); wherein the use of PCR amplification of a target gene with universal primers is followed by sequencing and comparison with the available publicly databases (i.e. reading on the second phase – sequencing comparison)( (pg. 171 para. 3).
• Capote does not teach “wherein if the resistance marker does not occur in any of the sequences of the nucleic acids or peptides in the sample or occurs in a number of nucleic acids that is smaller than a predefined minimum number then outputting a notification indicating that no sign of a resistance was found for the identified pathogen; wherein if the resistance marker occurs in a minimum number of sequences or in a number greater than the predefined minimum number then outputting a notification indicating that a sign of resistance was found for the identified pathogen, and outputting a notification about the resistance”. However, Luvisi teaches electronic identification web-based tools in plant pathology for storing, updating and sharing information (pg. 7 para. 1); wherein the assay activity diagram shows a step where detailed results for assay setup by the user is shared to all users and laboratories (i.e. notification outputted could comprise any type of information the user desires) in both cases where the sample has a positive identification or negative identification for the pathogen (pg. 12 Fig. 3 and pg. 13 col. 1 para. 3); wherein the method is also used to identify the presence or absence of infection markers for virus detection (pg. 9 col. 2 para. 1). Furthermore, Meyers teaches a method for similarity searches for sequences encoding resistance genes wherein a threshold expectation value was set to 0.0001 to filter out irrelevant hits (pg. 330 col. 1 para. 1).
Claim 7 recites:
collecting the sample of the plant or of the medium in which the plant is growing; identifying the pathogen in the sample; ascertaining at least one resistance marker for the identified pathogen and ascertaining a resistance-free sequence for the identified pathogen; and identifying signs of resistance of the identified pathogen to the control agent by comparison of the sequences of nucleic acids or peptides in the sample with the at least one ascertained resistance marker and the resistance-free sequence; wherein if a sequence or a number of sequences that is greater than or equal to a minimum number does not have a match with either the at least one resistance marker or the resistance-free sequence then outputting a notification indicating that a pathogen having a mutation pointing to a new and/or spreading resistance was identified in the sample
• Capote teaches that molecular identification of plant pathogenic fungi is accomplished by PCR amplification of internal transcribed spacer region followed by either restriction analysis or direct sequencing (i.e. ascertaining a target sequence for the identified pathogen) and BLAST searching against GenBank or other databases (i.e. identifying signs of a new resistance of the identified pathogen to the control agent by comparison of the sequences of nucleic acids or peptides in the sample with the target sequence) (pg. 155 para. 3); wherein fungal sequences in publicly accessible sequence databases, and sequences of selected genes (i.e. markers) have been widely used for the identification of specific pathogens (pg. 171 para. 3); wherein polymorphisms detected in the microsatellite flanking regions of Phytophthora infestans fungi allowed the development of a single nucleotide polymorphism genetic marker system for typing this pathogen (i.e. comparing the sequences of the nucleic acids or peptides in the sample with the at least one ascertained resistance marker) (pg. 157 para. 1); wherein primers are designed to detect and identify Verticillium dahliae and V. alboatrum and to distinguish pathogenic and non-pathogenic Fusarium oxysporum in tomato (i.e. matching pathogenic and non-pathogenic sequences – first phase – where the non-pathogenic sequences reads on comparisons yielding a non-match) (pg. 156 para. 2); wherein the use of PCR amplification of a target gene with universal primers is followed by sequencing and comparison with the available publicly databases (i.e. reading on the second phase – sequencing comparison)( (pg. 171 para. 3).
• Capote does not teach “wherein if the resistance marker does not occur in any of the sequences of the nucleic acids or peptides in the sample or occurs in a number of nucleic acids that is smaller than a predefined minimum number then outputting a notification indicating that no sign of a resistance was found for the identified pathogen; wherein if the resistance marker occurs in a minimum number of sequences or in a number greater than the predefined minimum number then outputting a notification indicating that a sign of resistance was found for the identified pathogen, and outputting a notification about the resistance”. However, Luvisi teaches electronic identification web-based tools in plant pathology for storing, updating and sharing information (pg. 7 para. 1); wherein the assay activity diagram shows a step where detailed results for assay setup by the user is shared to all users and laboratories (i.e. notification outputted could comprise any type of information the user desires) in both cases where the sample has a positive identification or negative identification for the pathogen (pg. 12 Fig. 3 and pg. 13 col. 1 para. 3); wherein the method is also used to identify the presence or absence of infection markers for virus detection (pg. 9 col. 2 para. 1). Furthermore, Meyers teaches a method for similarity searches for sequences encoding resistance genes wherein a threshold expectation value was set to 0.0001 to filter out irrelevant hits (pg. 330 col. 1 para. 1).
Rationale for combining (MPEP §2142-2143)
Regarding claims 6-7, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Capote in view of Luvisi and Meyers because all references disclose methods for investigating pathogen detection in plants. The motivation would have been to:
• support research data management and interaction between users in the detection of pathogen in plants (pg. 7 para. 1 Luvisi) and
• incorporate the investigation of characteristic domains of many plant resistance gene products (pg. 317 col. 1 para. 1 Meyers).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the method for the investigating pathogen detection of Capote to the methods by Luvisi and Meyers because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for investigating pathogen detection in plants.
E. Claims 11 is rejected under 35 U.S.C. 103(a) as being unpatentable over Capote as applied to claim 1 on the 102 rejection further in view of Cornelius (“A comparison of methods to estimate seasonal phenological development from BBCH scale recording” Int. J. Biometeorol. 55:867–877 (2011)), as cited on the 11/17/25 Form PTO-892. Any newly recited portions are necessitated by claim amendment.
Claim 11 recites:
wherein the plant is in principal growth stage 1 or 2 or 3 to 6 according to a BBCH scale.
• Capote does not explicitly teach the recited limitation above However, Cornelius teaches the description of the phenological growth stages of wild grasses according to the BBCH code for cereals including a plurality of species in principal growth stages 1 and 4-6 (pg. 870 Table 1).
Rationale for combining (MPEP §2142-2143)
Regarding claim 11, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Capote in view of Cornelius because all references disclose methods for investigating plants properties during development. The motivation would have been to enable the investigation of development cycle of plants (pg. 867 col. 1 para. 1 Cornelius) and improve statistical estimates (pg. 875 col. 2 para. 4 Cornelius).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the method for the investigating plants properties during development of Capote to the methods by Cornelius because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for investigating plants properties during development.
Response to applicant's remarks in regard to Claim Rejection 35 U.S.C. ~ 102/103
The Remarks of 02/17/2026 have been fully considered but are not persuasive for the reasons below:
Applicant asserts in pg. 14 para. 1:
Here, Capote fails to disclose an element of the claimed method, namely the dynamic, real-time, two-phase sequencing process. Independent claim 1, and its dependent claims, recite a specific, two-phase sequencing method wherein: 1. In a first phase, during the sequencing of an individual nucleic acid or peptide, the growing sequence is compared with at least one pathogen sequence; 2. If the growing sequence does not match, the sequencing of that specific nucleic acid or peptide is aborted; and 3. If a match is found, a switch is made to a second phase where the sequence is then compared against a resistance marker. … Nowhere does Capote teach or suggest the core inventive concept of making a comparison during the sequencing of an individual molecule and then aborting that specific sequencing run mid-process based on the outcome of that real-time comparison … Because Capote fails to teach, or even suggest, the critical limitations of comparing a growing sequence in real-time and aborting the sequencing of non-matching molecules before switching to a second analytical phase, Capote cannot anticipate claim 1. As independent claim 1 is not anticipated, dependent claims 2, 3, 10, 12, and 14, which add further limitations to the method, likewise cannot be anticipated
It appears that these remarks address the prior art not anticipating certain limitations under 35 U.S.C. 102. The Examiner disagrees and notes that claims 1, 5-9, 13 and 15-16 recites “if” statements which represent on contingent limitations (MPEP 2111.04.II) because the limitations only exist if a condition is met; causing the limitations to be non-requirements. See MPEP 2111.04 which states "If the claimed invention may be practiced without either the first or second condition happening, then neither step A or B is required by the broadest reasonable interpretation of the claim." If the Applicant intends for the contingent limitations to have patentable weight, then it is suggested to amend the claims to require their performance. In the case the claims actually affirmatively recite "aborting the sequencing based on the results", then there would be evidence for a practical application.
Applicant asserts in pg. 15 para. 6:
Here, the Examiner has rejected the claims over Capote, but then explicitly relies on Balzer as "evidence" to teach the limitations related to the system components, such as control units, calculation units, and data storage. By using Balzer to supplement the teachings of Capote, the Examiner has made an improper combination of references for an anticipation rejection. Such a combination may be the basis for an obviousness rejection under 35 U.S.C. § 103, not an anticipation rejection under§ 102. On this procedural basis alone, the rejection is deficient and should be withdrawn. Capote discloses the general commercial availability of next-generation sequencing instruments (Capote, p. 171, para. 4) but provides no teaching of their internal architecture or any specific control logic. Balzer, for its part, discloses a simulator for 454 pyrosequencing data (Balzer, Abstract). Its purpose is to generate realistic simulated data, not to provide a control system for a physical sequencer that performs a real-time analytical workflow. Balzer does not teach or suggest a control unit configured to receive a growing sequence, compare it to a pathogen database, abort the sequencing run if there is no match, and switch to a resistance checking phase if there is a match. Neither Capote nor Balzer, whether taken alone or in combination, discloses the specifically configured control and calculation unit claimed in claim 15 and which is embodied in the commands of claim 16. The cited references lack any teaching of the specific algorithmic logic that comprises the claimed invention
It appears that these remarks address the prior art not teaching certain limitations due to the use of evidentiary art. However, the Examiner disagrees and reaffirms that Capote teaches next-generation sequencing technologies commercially available for detection of plant pathogenic fungi and fungicide resistance include the 454 GS20 pyrosequencing-based instruments, the Solexa 1G analyzer and the SOLiD instrument. The technologies taught by Capote inherently possess the architecture of a sequencing unit; a control and calculation unit with data and storage capacity configured to receive a growing sequence calculate values and compare it to a pathogen database; which is evidenced by the prior art to Balzer. In this manner, the Examiner did apply evidentiary rejection correctly. Therefore, the cited references do not lack any teaching of the specific algorithmic logic that comprises the claimed invention. MPEP 2131.01.II pertains.
Regarding the argument that Blazer does not teach a control system for a physical sequencer, the Examiner notes that Blazer teaches the inherent function an algorithm applied in 454 sequencer system which applies an algorithm for base calling and alignment (i.e. sequencing steps performed in the sequencer), reading on the function of a control unit for a sequencer (pg. i420 col. 1 para. 5).
Applicant asserts in pg. 17 para. 2:
The "real-time" abort element of claim 1 is discussed above at page 12 (Section V). For reasons of (relative) brevity, Applicant will not represent those arguments here. Neither Capote nor Meentemeyer, alone or in combination, teach or suggest this specific technical process. Capote teaches various molecular tools for detecting pathogens, including sequencing followed by BLAST searching against databases (Capote, p. 155, para. 3). … However, there is no teaching, suggestion, or motivation in the combined art (either explicit or inherent) that would lead the skilled artisan to fundamentally re-engineer the sequencing process of Capote to include the real-time comparison and abortive step as claimed - which is regardless not disclosed by either reference. … The combination of Capote Meentemeyer does not teach aborting the sequencing of non-pathogen nucleic acids in real-time, as recited by the rejected claims (via claim 1). Regarding claim 13, this claim depends from claim 1 and further recites creating, updating, and outputting a pathogen map, for which the Examiner cites Meentemeyer. As with the arguments for claim 4, while Meentemeyer teaches GIS mapping (Meentemeyer, Abstract), claim 13 is nonobvious over the combination because it also depends on the novel and nonobvious method of claim 1. The combination of Capote Meentemeyer simply does not teach or suggest generating pathogen data in this particularly efficient manner recited in claim 1 for display on a map
It appears that these remarks address the combination of the teachings by the prior art to Capote Meentemeyer not teaching certain limitations. While none of the references teach all claim limitations, and the examiner does not dispute Applicant's identification of material missing from Capote, all the claim limitations are taught by the combination of references, as explained in the Claim Rejections above. "One cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references" (MPEP 2145 § IV). This argument is unpersuasive, because it analyzes the teachings of the references separately and independently, whereas the rejection is based on the combined teachings of the references. The deficiencies identified regarding the "real-time" abort element of claim 1 have been addressed in the Claim Rejections with teachings by Capote . Claims 1, 5-9, 13 and 15-16 recites “if” statements which represent on contingent limitations (MPEP 2111.04.II) because the limitations only exist if a condition is met; causing the limitations to be non-requirements. See MPEP 2111.04 which states "If the claimed invention may be practiced without either the first or second condition happening, then neither step A or B is required by the broadest reasonable interpretation of the claim." If the Applicant intends for the contingent limitations to have patentable weight, then it is suggested to amend the claims to require their performance. In the case the claims actually affirmatively recite "aborting the sequencing based on the results", then there would be evidence for a practical application.
Meentemeyer combines additional teachings about parameters used to predict the locations of new infections, with accuracies ranging from 0.86 to 0.90 (pg. 377 para. 1); wherein habitat and spatial position variables are digitally mapped (i.e. wherein a location is recorded in the pathogen map) serving for guiding management with resulting model equations being applied and visualized in a geographic information system (i.e. displaying on a screen) (pg. 378 col. 1 para. 2); wherein new detections discovered through our sampling were also continually added to this data set (i.e. updating the pathogen database/map) (pg. 381 col. 2 para. 1). Regarding the teachings by Meentemeyer, one of ordinary skill in the art would be motivated to apply the teachings by Meentemeyer to the method by Capote to incorporate probabilistic modeling to analyze the relative roles of niche and dispersal limitation in controlling the distribution of invasive pathogens (pg. 377 para. 1 Meentemeyer). The prima facie case of obviousness has been established. MPEP 2141.III for "RATIONALES TO SUPPORT REJECTIONS UNDER 35 U.S.C. 103"; wherein "(G) Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention.".
Applicant asserts in pg. 18 para. 6:
The Examiner's combination of Capote Luvisi is improper because it attempts to use a passive, user-driven data-sharing tool (Luvisi) to supply a concept recited in the claims: an automated system with specific, conditional process logic. The claimed invention is not merely a method for sequencing followed by a tool for reporting; it is an integrated and active analytical engine. …The combination of Capote Luvisi could reasonably result in a method where a scientist performs the Capote analysis, manually interprets the results, and then uses a system like Luvisi to type and share a message. Luvisi's system is merely a conduit for user-generated information and provides no teaching on how to build a system that automates the link between the analytical result and the specific output, as claimed. … The Examiner's reliance on the "obvious to optimize" rationale is misplaced. Identifying a previously unknown, functionally significant mutation is a matter of discovery, not mere optimization of a known process for a predictable result. A person of ordinary skill would have no reasonable expectation that modifying Capote's method to look for any and all mutations would successfully identify a new form of resistance. The problem solved by claim 8-the discovery and flagging of novel resistance mechanisms-is fundamentally different from the problems solved by the cited prior art. The combination provides no teaching or motivation (either inherent or explicit) to build such a discovery-oriented analytical tool
It appears that these remarks address the prior art to Capote Luvisi not teaching certain limitations. However, the Examiner disagrees because the sharing tool taught by Luvisi does implement the argued automation aspect of the claimed invention. Luvisi teaches that the taught method allows lab systems to move from isolated data stations toward more effective and integrated laboratory automation (pg. 15 col. 1 para. 3). The motivation to optimize is correctly applied to the recited “identifying signs of a new resistance”. Considering the taught steps for identifying an initial sign of resistance, one can be motivated to optimize such method for the identification of other signs. A motivation to use the same steps already taught to find a new resistance originates from the “obvious to optimize” 2144.05 rationale ,which states that choosing from a finite number of identified, predictable solutions (i.e., in this case a finite number of steps already established to identify a plant pathogen/resistance), with a reasonable expectation of success would motivate one of ordinary skill in the art. See MPEP 2143 (I).
Applicant asserts in pg. 20 para. 3:
As noted above, claim 1 recites a specific, two-phase sequencing method including a "conditionally abortive" step, which is entirely undisclosed and not suggested by Capote Luvisi. The Examiner's proposed combination of Capote, Luvisi, and Meyers is wholly devoid of this teaching. Capote discloses a conventional "sequence-then-analyze" method. Luvisi discloses a user-driven data-sharing platform. The newly added reference, Meyers, also only discloses a post-sequencing analysis step-specifically, using a statistical threshold to filter the results of a database search. See Meyers, Abstract. Meyers provides absolutely no teaching or suggestion of modifying the sequencing apparatus itself to perform a comparison in real-time or to abort the sequencing of a single molecule mid-process. Because the new combination of Capote, Luvisi, and Meyers still fails to teach or suggest the conditionally abortive sequencing process of claim 1, the combination cannot provide a prima facie case of obviousness against claim 1. Accordingly, the combination necessarily fails to render dependent claims 6 and 7
It appears that these remarks address the prior art to Capote, Luvisi and Meyers not teaching certain limitations. Arguments regarding Capote lacking the teaching about the recited "if the ascertained sequence does not match the at least one pathogen sequence, further sequencing of said nucleic acid or said peptide is aborted" have been addressed previously. The described deficiency is now addressed by Capote in the Claim Rejections above. Claims 1, 5-9, 13 and 15-16 recites “if” statements which represent on contingent limitations (MPEP 2111.04.II) because the limitations only exist if a condition is met; causing the limitations to be non-requirements. See MPEP 2111.04 which states "If the claimed invention may be practiced without either the first or second condition happening, then neither step A or B is required by the broadest reasonable interpretation of the claim." If the Applicant intends for the contingent limitations to have patentable weight, then it is suggested to amend the claims to require their performance. In the case the claims actually affirmatively recite "aborting the sequencing based on the results", then there would be evidence for a practical application.
Furthermore, regarding claims 6-7, the detailed explanation of subject matter suggested by a prior art reference to Luvisi and Meyers is entirely acceptable when establishing a rationale for obviousness: "to support the conclusion that the claimed invention is directed to obvious subject matter, either the references must expressly or impliedly suggest the claimed invention or the examiner must present a convincing line of reasoning as to why the artisan would have found the claimed invention to have been obvious in light of the teachings of the references" (Ex parte Clapp, 227 USPQ 972 at 973 (BPAI 1985)); "Office personnel may also take into account 'the inferences and creative steps that a person of ordinary skill in the art would employ' (KSR v. Teleflex Inc., 82 USPQ2d 1385 at 1396 (SC 2007))" (MPEP 2141 § 11.C); "the rationale to support a rejection under 35 U.S.C. 103 may rely on logic and sound scientific principle" (MPEP 2144.02). The examiner's explanation of how the combination of teachings read over the claimed invention presents a convincing line of reasoning, takes into account and explains the inferences and creative steps by a person of ordinary skill in the art, and relies on logic and sound scientific principle.
Applicant asserts in pg. 21 para. 3:
As noted above, claim 1 recites a specific, two-phase sequencing method including a "conditionally abortive" step, which is entirely undisclosed and not suggested by Capote. The Examiner's proposed combination of Capote Cornelius is wholly devoid of this teaching. Capote discloses a conventional "sequence-then-analyze" method. The newly added reference, Cornelius, is directed to the field of phenology and teaches the use of the BBCH scale for classifying plant growth stages. See Cornelius, Abstract. Cornelius provides no teaching whatsoever related to sequencing technology, much less a method for controlling a sequencing process in real-time to conditionally abort the sequencing of individual molecules. Because the new combination of Capote Cornelius still fails to teach or suggest the conditionally abortive sequencing process of claim 1, the combination cannot provide a prima facie case of obviousness against claim 1. Accordingly, the combination necessarily fails to render dependent claim 11
It appears that these remarks address the prior art to Capote Cornellius not teaching certain limitations. However, the Examiner disagrees because there is sufficient suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention. Cornelius is indeed directed to the field of phenology and teaches the use of the BBCH scale for classifying plant growth stages. In the field of method for investigation of plant properties being affect by the presence of pathogens, one can be motivated to use the teachings by Cornellius regarding the use of the BBCH scale to enable the investigation of development cycle of plants (pg. 867 col. 1 para. 1 Cornelius) and improve statistical estimates (pg. 875 col. 2 para. 4 Cornelius). Therefore, the prima facie case of obviousness has been established. MPEP 2141.III for "RATIONALES TO SUPPORT REJECTIONS UNDER 35 U.S.C. 103."
No prior art has been applied to the following claims
Claim 9 appear to be free of the analogous art at least because close art, e.g. Capote, Meentemeyer, Luvisi, Meyers and Cornellius, as cited in the 11/17/25 Form PTO-892, either individually or in obvious combination, does not teach the recited combination of particular steps/elements regarding the recitation below:
ascertaining a frequency QR of nucleic acids or peptides found in the sample that have a sequence according to the resistance marker, ascertaining a frequency QNR of nucleic acids or peptides found in the sample that have a sequence according to the resistance-free sequence, calculating a ratio of the ascertained frequencies QR and QNR, and comparing the ratio with a predefined minimum value; wherein if the ratio is greater than or equal to the predefined minimum value then outputting a notification indicating that a sign of a resistance was found for the identified pathogen, and outputting a notification about the resistance
Conclusion
No claims are allowed.
Claim 14 appear to be free from 101 issues due to the recited “ascertaining a control agent for controlling the identified pathogen, taking into account the resistance that may have been identified; and carrying out a measure to control the pathogen in the plant using the ascertained control agent”; which constitutes evidence of how the judicial exception is impacted by the additional element; reading on a practical application under step 2A Prong 2.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/F.F.L./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685