DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 1/29/2026 has been entered.
The claims 112 and 13 has been amended. Claims 5-8, 10 has been canceled. Claims 1-4, 9 and 11-13 are pending. The claim rejections under 35 USC 112(b) are withdrawn in view of Applicant’s amendment of the claims. The claim rejections under 35 USC 101 are withdrawn in view of Applicant’s amendment and arguments. The prior art rejection under 35 USC 103 is maintained but modified to address Applicant’s amendments.
All claims are patentably indistinct from, or have unity of invention with claims in the application prior to the entry of the submission under 37 CFR 1.114 (that is, restriction (including a lack of unity of invention) would not be proper) and all claims could have been finally rejected on the grounds and art of record in the next Office action if they had been entered in the application prior to entry under 37 CFR 1.114. Accordingly, THIS ACTION IS MADE FINAL even though it is a first action after the filing of a request for continued examination and the submission under 37 CFR 1.114. See MPEP § 706.07(b). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
Declaration
The Declaration under 37 CFR 1.132 filed 1/29/2026 is insufficient to overcome the rejection of claims 1-4, 9, 11-13 based upon a 35 USC 103 rejection as set forth in the last Office action.
Expert’s Traversal
The Expert traverses the rejection on the following grounds:
(a) The Expert summarized the claimed invention and disclosed that the presence application discloses, “RNA molecules may exist in higher copy number in a cell as compared with corresponding DNA, but are degraded easily in general and therefore appear more unlikely to remain in the environment than DNA (specification at paragraph [0004]). The Expert states that in other words, it is stated that the fast degradation of RNA does no necessarily lead to reduction in false positives. The expert states that it is support by Exhibits 1-6 and provides a summary for each of the exhibits cited.
(b) The Expert states that it is their opinion that Exhibits 1-6 further support tht the fast degradation of RNA does not necessarily lead to reduction in false positives.
Examiner’s response
All of the amendment and arguments have been thoroughly reviewed and considered but are not found persuasive for the reasons that follow:
(a) Regarding the arguments at (a) and (b) above, the Examiner respectfully acknowledges Applicant’s arguments but notes that the arguments are not commensurate fully in scope with the claims as currently pending. Specifically, the claims 1-4, 9, 11-13 in the claim 1 recite at steps (iii) and (iv) wherein “(iii) identifying the biological species living in the water environment by comparing results of the analysis of the RNA and results of the analysis of the DNA; and (iv) identifying false positive biological species by determining a ratio between a quantitative value of the RNA and a quantitative value of the DNA for each identified biological species”. The claims, as broadly written, do not require any specific with regard to the way in which false positive biological species are identified but only requires that “a ratio be determined between quantitative values of RNA and DNA”. The claims, when interpreted as whole, do not exclude fast degradation of RNAs as it relates to false positive or include and/or recite any specific criteria for reducing false positive. Rather the claims only require determining a ratio that may identify false positive. Further while the Expert’s exhibits 1-6 provides some evidence that fast degradation of RNA does not necessarily lead to reduction in false positive, the evidence does not exclude the comparison of results of eRNA and eDNA being capable of identifying false positives and in turn identifying a biological species. It is noted that although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
Finally, the examiner notes, the court [in O'Farrell] stated: '[o]bviousness does not require absolute predictability of success ... all that is required is a reasonable expectation of success."'Kubin, 561 F.3d at 1360 (citing In re O'Farrell, 853 F.2d at 903-904). The examiner maintains that the combination of the cited prior art provides a prima facie case that the combination of the cited prior art could results in identifying false positives by analyzing quantitative results of RNA and DNA and using the information to identify biological species. The declaration by the Expert is not persuasive to withdrawn the prior art rejection under 35 USC 103 as being unpatentable over the teachings of Pochon et al in view of Ammon et al.
Claim Rejections - 35 USC § 103
8. The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Note* The following grounds of rejections have been modified to address Applicant’s amendment of the claims. Although the claims were previously rejected as being unpatentable over the same reference(s), Applicant's amendments have necessitated the inclusion of these grounds of rejections in this Office action. Applicant's arguments are addressed following the rejection.
9. Claim(s) 1, 2, 3, 4, 9, 11, 12 and 13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Pochon et al., {Pochon recited herein} (PLOS ONE, 12(11): e0187636, 1-19, Nov. 2017) in view of Ammon et al (Frontiers in Marine Science, 6(621), 1-13, October 2019).
Regarding claim 1, Pochon teaches a method for analyzing biological species living in a water environment, comprising: i) analyzing RNA contained in the water environment quantitatively, (ii) analyzing DNA contained in the water environment quantitatively (iii) identifying the biological species living in the water environment by comparing results of the analysis of the RNA and results of the analysis of the DNA (See pages 4-7). Pochon teaches wherein the analysis of the RNA is performed by metabarcoding of the RNA (pages 4-6). Pochon further teaches wherein the metabarcoding of the RNA comprises:(i) obtaining a sample from the water environment; (ii) extracting the RNA from the sample; (iii) converting the RNA to cDNA by reverse transcription; (iv) preparing a library by selectively amplifying a region of the cDNA by PCR; (v) sequencing the library; and (vi) comparing the library against known genome sequences for biological species (pages 4-7 and figures showing sample analysis).
With regards to the step of (iv) identifying false positive biological species by determining a ratio between a quantitative value of the RNA and a quantitative value of the DNA for each identified biological species, Pochon teaches bioinformatics and statistical analyses along with figures which shows methods steps of analyzing data to filter out incorrect or false positive results (see pages 5-6 and Figures).
Regarding claim 2, Pochon teaches wherein the analysis of the RNA is performed by next-generation RNA sequencing (pages 4-6).
Regarding claims 3 and 4. Pochon teaches wherein the biological species include fish (page 7, which teaches identification of a bony fish Auxis spp.).
Regarding claim 9, Pochon teaches wherein the water environment bilge sample water from coastal harbors and bays from marinas in Nelson and Picton, New Zealand (pages 3-4).
Regarding 11, Pochon teaches wherein the analysis of the DNA is performed by metabarcoding of the DNA (pages 4-6).
Regarding 13, Pochon teaches wherein the RNA comprises a region that can be selectively amplified by PCR (18S rRNA region) (page 4).
Regarding claim 1 and 12, Pochon does not expressly teach calculating the false positives based on the determining a ratio between a quantitative value of the RNA and a quantitative value of the DNA for each identified biological species in the water sample.
In a similar embodiment, Ammon et al teach a method of analyzing eDNA and eRNA to detect marine invasive organisms in water sample, the method comprising analyzing RNA contained in the water environment quantitatively, (ii) analyzing DNA contained in the water environment quantitatively (iii) identifying the biological species living in the water environment by comparing results of the analysis of the RNA and results of the analysis of the DNA (See pages 3-5). Regarding false positive determination, Ammon teaches that the principle of ROC analysis is to plot the relation between the true positive rate (y-axis), against the false positive rate (x-axis), Ammon states that the true positive rate gives the sensitivity or probability of detection, while the false positive rate or the probability of a false positive detection is calculated as 1 – specificity (where “specificity” is calculated as the ratio of the true negatives divided by the true negatives plus false positives, which are derived from consistent values among DNA and RNA detections per sample). The area under the curve (AUC) is a measure of the response to predictor, with 100% value indicating perfect prediction. The most sensitive and specific response (the most upper left value in the curve) indicates the optimal predictor threshold value (page 4, col. 2, last paragraph).
Ammon additionally teach for metabarcoding analyses, singletons were discarded and samples were grouped into the water or plate datasets, from which two datasets were created: 1) ASVs found in RNA extracted samples (i.e., cDNA), hereafter referred to as “eRNA” and 2) ASVs found in DNA-extracted samples, hereafter referred to as “eDNA.” Venn diagrams were created using Venny to visualize the proportion of overlapping ASVs within each dataset. Bar plots were created based on the relative abundance of the above-mentioned datasets summed at the phylum level using the R package “phyloseq”. For alpha and beta-diversity analysis, metabarcoding datasets were rarefied to 5,000 reads per sample (Supplementary Figure S3) and Principal coordinate analysis (PCO) was performed on the “eRNA” and “eDNA” datasets to visualize differences between plate and water samples (page 4, col. 1). Ammon teaches that with regards to detecting results, the total number of raw COI reads obtained for the 36 eDNA and 36 eRNA amplicons, were 3,027,021 and 2,688,149, respectively. These resulted in 730,210 and 593,468 paired-end, quality filtered and non-chimeric sequences comprising 3671 and 1872 ASVs excluding singletons (page 5, col. 2).
In view of teachings of Pochon and Ammon, it would have been obvious to one of ordinary skill in the art at the time of the effective filing date of the claimed invention to have easily conceive determining false positive and calculating quantitative eDNA and eRNA values as taught by Ammon in the detection method of Pochon for the obvious benefit of improving means for detecting and analyzing biological species living in a water sample.
Response to Arguments
Applicant’s traversal
10. Applicant traverses the rejection on the following grounds:
(a) Applicant summarizes the Examiner’s rejection and states that no prima facie case of obviousness exists in the present matter because obviousness requires proof that such a person would have a reasonable expectation of success in modifying or combining the cited art to achieve the claimed invention. Applicant states that the Examiner has not established that the claimed method for analyzing biological species living in a water environment is prima facie obvious.
(b) Applicant states that in contrast to the claimed ration, Ammon’s ratio requires prior knowledge of the true negatives and false positives to even be calculated.
(c) Applicant states that the Examiner alleges that false positives are naturally reduced because RNA degrades faster than DNA, however notes that nucleic acids remaining in the environment are not determined solely by degradation rate, but also based on the amounts of DNA and RNA and the amounts are typically not equivalent. Applicant states that the present application provides evidence that the fast degradation of RNA does not necessarily lead to reduction in false positives.
(d) Applicant states that the presence application discloses comparisons between eRNA and eDNA reveals that eRNA reduces false positives and that use of the eRNA/eDNA ration enables analysis of contamination sources and identification of false positives (citations noted).
(e) Applicant discuss Example 3 and discuss that the example shows that the advantage of eRNA is not attributable merely to its faster degradation, but experimental results indicate that composite factors such as origin of input, initial amounts and outflow conditions.
(d) Applicant states that Applicant asserts that it is inappropriate to drawn conclusions solely from degradation rate while disregarding difference in initial quantities. Applicant states that initial amount of eDNA and eRNA should be considered. Applicant state that the analysis of the presence invention combines eRNA with eDNA rather than relying on eRNA alone enable identification of contamination sources and exclusion of false positives. Applicant states that furthermore, ROC analysis provides quantitative evidence (AUC values) showing that eRNA and the eNA ratio are superior to eDNA in excluding false positives. This special technical effect cannot be explained merely by degradation rate. Applicant concludes that a prima facie case of obvious has not been met.
Examiner’s Response
11. All of the amendment and arguments have been thoroughly reviewed and considered but are not found persuasive for the reasons that follows:
i. In regards to Applicant arguments at a) concerning proof of obviousness, Applicant is reminded that KSR forecloses the argument that a specific teaching, suggestion, or motivation is required to support a finding of obviousness. See the Board Decision Ex parte Smith, --USPQ2d--, slip op. at 20, (Bd. Pat. App. & Interf. June 2007) (citing KSR, 82 USPQ2d at 1396).
Further the Court commented that "[r]esponding to concerns about uncertainty in the prior art influencing the purported success of the claimed combination, this court [in O'Farrell] stated: '[o]bviousness does not require absolute predictability of success ... all that is required is a reasonable expectation of success."' Kubin, 561 F.3d at 1360 (citing In re O'Farrell, 853 F.2d at 903-904). Thus is argument is not found persuasive.
ii. In regards to Applicant’s arguments at (b) –(d), the examiner acknowledges Applicant’s arguments but notes that the arguments are not commensurate fully in scope with the claims as currently written. Given the broadest reasonable interpretation, the claims as written do not require any specifics with regard to the way in which false positive biological species are identified but only requires that “a ratio be determined between quantitative values of RNA and DNA”. The claims, when interpreted as whole, do not exclude fast degradation of RNAs as it relates to false positive or include and/or recite any specific criteria for reducing false positive. Rather the claims only require determining a ratio that may identify false positive. Further while the Expert’s exhibits 1-6 provides some evidence that fast degradation of RNA does not necessarily lead to reduction in false positive, the evidence does not exclude the comparison of results of eRNA and eDNA being capable of identifying false positives and in turn identifying a biological species. It is noted that although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
iii. Further with regards to Applicant’s comments at (c) and (d) concerning relying on eRNA alone for detecting false positives, this argument is not found persuasive because the teaching of Ammon et al teach at page 4 that under statistical analysis was based on DNA and RNA detects per samples. Both reference discusses analysis of both RNA and DNA, including determining amount(s) gleaned from PCR and sequencing analyses in environmental samples (see entire documents of Pochon an Ammon). In view of the foregoing, Applicant’s arguments are not found persuasive to overcome the prior art teachings of Pochon in view of Ammon.
Conclusion
12. No claims are allowed. All claims are patentably indistinct from, or have unity of invention with claims in the application prior to the entry of the submission under 37 CFR 1.114 (that is, restriction (including a lack of unity of invention) would not be proper) and all claims could have been finally rejected on the grounds and art of record in the next Office action if they had been entered in the application prior to entry under 37 CFR 1.114. Accordingly, THIS ACTION IS MADE FINAL even though it is a first action after the filing of a request for continued examination and the submission under 37 CFR 1.114. See MPEP § 706.07(b). 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.
13. Any inquiry concerning this communication or earlier communications from the examiner should be directed to CYNTHIA B WILDER whose telephone number is (571)272-0791. The examiner can normally be reached Flexible.
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/CYNTHIA B WILDER/Primary Examiner, Art Unit 1681