DETAILED CORRESPONDENCE
Status of the Application
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1 and 4-15 are pending.
Applicant’s amendment to the claims filed 05/26/2026 is acknowledged. This listing of the claims replaces all prior versions and listings of the claims.
Applicant’s amendment to the specification filed 05/26/2026 is acknowledged.
Applicant’s amendment to the drawings filed 05/26/2026 is acknowledged.
Applicant’s remarks filed on 05/26/2026 in response to the non-final rejection mailed on 03/05/2026 are acknowledged and have been fully considered.
The rejections to claims 2-3 are withdrawn in view of the cancelation of the claims.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Election
The elected subject matter is:
Group I, corresponding to claims 1 and 4-15, drawn to the technical feature of a method for detecting the presence of a bacterial and/or fungal cell in a sample comprising detecting the presence of nicotinamidase activity or nicotinamidase, wherein the presence of nicotinamidase activity or nicotinamidase indicates the presence of a bacterial and/or fungal cell in the sample; the technical feature of a method for assessing the sterility of a sample comprising detecting the presence of nicotinamidase activity or nicotinamidase in the sample, wherein the lack of nicotinamidase activity or nicotinamidase as compared to a reference indicates that the sample is sterile, sterilized or free from bacterial and/or fungal cell contamination; and the technical feature of a method for monitoring bacterial and/or fungal cell contamination in a cell or tissue culture, comprising detecting the presence of nicotinamidase activity or nicotinamidase in the cell or tissue culture, wherein the presence of nicotinamidase activity or nicotinamidase indicates bacterial and/or fungal cell contamination in the cell or tissue culture.
elected without traverse in the reply filed 01/24/2026 is acknowledged.
Claims 1 and 4-15 are being examined on the merits.
Objections to Specification
The objection to the specification is withdrawn in view of the amendments to address the use of trademarks.
Objections to Drawings
The objections to the drawings are withdrawn in view of the Drawings filed 05/26/2026 to distinctly label the panels in Figure 15 and the amendments to the specification to describe the structural details of Figure 3.
Claim Objections
The objection to claim 9 is withdrawn in view of the amendment to recite “wherein the bacterial and/or fungal cell comprises a PncA gene”.
Claims 6 and 12 are objected to for the typo in the phrase “wherein the determining the levels of”. In the interest of improving claim form, Applicant should consider amendments to recite “wherein the determining of the levels of”.
Claim Rejections - 35 USC § 112(b)
Claims 1, 4-10 and 12-15 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
The instant rejection is maintained from the previous office action, any newly recited portions are necessitated by claim amendment.
Claims 1 (claims 4-10 and 12 dependent therefrom), 13 and 14 (claim 15 dependent therefrom) are indefinite for the recitation of “a reference”, as it is unclear from the claims and the specification as to the reference ratio level for comparison that is indicative of the presence of a bacterial and/or fungal cell in the sample.
Claim 6 recites the limitation “the nicotinamidase gene or gene expression product” in line 3. There is insufficient antecedent basis for this limitation in the claim.
Response to Remarks: beginning on page 13 of Applicant’s response to rejections under 35 USC 112(b); Applicant in summary contends the instant amendments overcome the rejection of record.
Applicant’s remarks are considered and found not convincing, as the claims still recite the indefinite phrase “the reference” recited in claims 13 and 14, and now amended into claim 1, and claim 6 still recites “the nicotinamidase gene or gene expression product” without antecedent basis.
Claim Rejections - 35 USC § 103
Claims 1, 4-5, 8 and 11-13 are rejected 35 U.S.C. 103 as being unpatentable over Oishi et al. (J Chromatog B, 1998, 720:59; cited on the IDS filed 10/26/2023; herein referred to as Oishi98).
The instant rejection is maintained from the previous office action, any newly recited portion is necessitated by claim amendment.
Claim 1 (claims 4-5, 8 and 11-12 dependent therefrom) is drawn to a method for detecting the presence of a bacterial and/or fungal cell in a tissue or cell culture sample, the method comprising
determining levels of nicotinic acid and nicotinamide in a tissue or cell culture supernatant sample,
wherein an increase in the ratio of nicotinic acid and nicotinamide levels as compared to a reference indicates the presence of a bacterial and/or fungal cell in the tissue or cell culture sample.
Claim 13 is drawn to a method for assessing the sterility of a tissue or cell culture sample, the method comprising
determining the levels of NA and NAA in a tissue or cell culture supernatant sample,
wherein an increase in the ratio of NA to NAA levels as compared to a reference indicates that the tissue or cell culture sample is free from bacteria and/or fungal cell contamination.
Oishi98 relates to assays of nicotinamide deaminase [title].
Regarding claim 1, Oishi98 discloses an assay of nicotinamide deamidase activity using high-performance liquid chromatography [title], wherein nicotinamide deamidase is understood to be an alternate name of the enzyme nicotinamidase that catalyzes deamidation of nicotinamide (NAA) to nicotinic acid (NA) [p 59, col 1, paragraph 1], and increases of NA attributed to nicotinamidase activity correspond to the presence of bacteria [p 59, col 1, final paragraph to col 2, 1st paragraph]. Therefore Oishi98 indicates the connection between increase NA:NAA levels in a sample to nicotinamidase activity from a bacteria.
Regarding claim 1 and the limitation of determining levels of NA and NAA in tissue or cell culture supernatant sample, Oishi98 discloses the determination of NA and NAA levels from meat-derived samples [Figure 2], wherein bacterial strains were isolated from meat samples, grown in cell culture media, and thereafter isolated cells were disrupted for the collection of supernatant that was referred to as crude extract [p 60, col 1, final paragraph to col 2, 2nd paragraph; and Figure 2 legend], and wherein the detection of increased NA from meat attributed to bacterial nicotinamidase activity [p 59, col 1, final paragraph to col 2, 1st paragraph]. Therefore the NA and NAA levels measured by Oishi98 are considered to correspond to the levels of NA and NAA from a cell culture supernatant.
Oishi98 additionally discloses that while NA and NAA are used to process foodstuffs, they are prohibited to be added to meat in Japan, and NA is usually absent in meat while NAA is present [p 59, col 1, para 2], which is considered to correspond to a ratio of NA:NAA in a reference sample. As the disclosure of the detection of increased NA from meat attributed to bacterial nicotinamidase activity is considered to correspond to an increase in the NA:NAA ratio compared to said reference, the disclosure of Oishi98 is considered to correspond to “an increase in the ratio of NA to NAA as compared to a reference indicates the presence of a bacterial and/or fungal cell in the sample” as recited in the claim.
In view of Oishi98, 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 determine the presence of a bacteria in a sample by detecting the presence of nicotinamidase by determining the levels of NA and NAA. One of ordinary skill in the art would have been motivated to detect the presence of nicotinamidase by determining the levels of NA and NAA because Oishi98 discloses increased amounts of NA in a sample can correspond to nicotinamidase activity due to the presence of bacteria in the sample. One of ordinary skill in the art would have had a reasonable expectation of success because of the express teachings of Oishi98.
Regarding claim 4, Oishi98 discloses the isolation of strains isolated from meat which possessed nicotinamide deamidation activity [p 60, col 1, para 3], which is considered to correspond to “the presence of live bacterial and/or fungal cells in the sample” as recited in the claim. Regarding claim 5, Oishi98 discloses the detection of NA and NAA via HPLC focusing on the absorption over time at 261 nm [Figure 1], which is considered to correspond to UV spectroscopy.
Regarding claim 8, Oishi98 discloses an assay of nicotinamide deamidase activity using high-performance liquid chromatography [title], wherein nicotinamide deamidase is understood to be an alternate name of the enzyme nicotinamidase that catalyzes deamidation of nicotinamide (NAA) to nicotinic acid (NA) [p 59, col 1, paragraph 1], and increases of NAA attributed to nicotinamidase activity correspond to the presence of bacteria [p 59, col 1, final paragraph to col 2, 1st paragraph]. Therefore the disclosure of Oishi98 is considered to correspond to the detection of a bacterial and/or fungal cell that comprises or expresses a nicotinamidase enzyme.
Regarding claim 11, Oishi98 discloses the detection of NA and NAA in meat samples from which bacteria are isolated, wherein the corresponding reference for comparison is meat known to lack NA as discussed in the rejections of claims 1 and 4 above. As the comparison of the NA:NAA levels of the sample to the corresponding reference identified the sample as having potential bacterial presence and subsequently resulted in the isolation of live bacteria from the sample, the corresponding reference is considered to not have bacterial and/or fungal contamination as recited in the claim.
Regarding claim 12, the instant specification does not specifically define contamination relevant to the number of detected bacterial and/or fungal cells, and therefore the plain definition of contamination is being used that corresponds to the presence of an impurity in a substance. In view of this interpretation, the disclosure of Oishi98 of the detection of bacterial and/or fungal cells from a sample with increased NA:NAA ratios as discussed in the rejection of claim 1 is considered to correspond to the detection of bacterial and/or fungal contamination in said sample, as Oishi98 additionally discloses that NA is not normally present in meats if not supplemented with a food additive, and therefore indicates that the bacteria responsible for generating the NA would be an impurity in the meat.
Regarding claim 13, Oishi98 discloses the method of detection nicotinamidase activity as described in rejection of claim 1 above that corresponds to the detection of the presence of bacterial and/or fungal contamination of a sample as described in the rejection of claim 12. As Oishi98 discloses the presence of the increased ratios of NA:NAA in the sample are not expected given the corresponding reference of meat only naturally contains NAA as discussed in the rejection of claim 1, the method of Oishi98 is considered to correspond to the detection of nicotinamidase activity, wherein the lack of nicotinamidase activity, corresponding to the known amounts of NA:NAA in the corresponding reference, indicates a sample is free from bacterial and/or fungal cell contamination. Put another way, as Oishi98 discloses the increased ratio of NA:NAA in comparison to a corresponding reference is associated with bacterial and/or fungal contamination of a sample, Oishi98 therefore implicitly discloses that a sample with the NA:NAA ratio similar to the corresponding reference would therefore be free of bacterial and/or fungal cell contamination.
Therefore, the invention of claims 1, 4-5, 8 and 11-13 would have been obvious to one of ordinary skill in the art before the effective filing date.
Claims 6-7 and 9 are rejected under 35 U.S.C. 103 as being unpatentable over Oishi98 as applied to claims 1, 4-5, 8 and 11-13, and further in view of Ramadan et al. (Global Veteranaria, 2012, 9:648; cited on the Form PTO-892 mailed 03/05/2026; herein referred to as Ramadan).
The instant rejection is maintained from the previous office action, any newly recited portion is necessitated by claim amendment.
Claim 6 is drawn to the method of claim 1, wherein the determining the levels of NA and NAA in the tissue or cell culture supernatant sample comprises detecting nicotinamidase which comprises detecting the nicotinamidase gene or gene expression product,
wherein the presence of nicotinamidase gene or gene expression product indicates the presence of a bacterial and/or fungal cell in the sample.
The teachings of Oishi98 as applied to claims 1, 4-5, 8 and 11-13 are discussed above. Oishi98 does not teach detecting the nicotinamidase gene or gene expression product.
Ramadan relates to the detection of Mycobacterium bovis and Mycobacterium tuberculosis from clinical samples [title], and discusses that determination of the presence of organisms in a sample via culturing has the disadvantage that may take 6-8 weeks and require viable organisms, wherein PCR amplification of DNA is a rapid and reliable method for rapid diagnosis of the presence of a target microorganism [p 648, col 2, para 1].
Regarding claims 6-7 and 9, Ramadan teaches the use of PCR to detect the PncA gene of M. tuberculosis [p 649, col 2, para 4] from sputum samples collected from clinically diagnosed patients for the identification of Mycobacterium spp. [p 649, col 1, final paragraph], wherein the PncA gene corresponds to gene encoding a nicotinamidase enzyme according to the instant specification [p 14, final paragraph].
In view of Ramadan, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date to modify the method of Oishi98 by detecting the PncA gene, as taught by Ramadan, to arrive at the claimed invention. One of ordinary skill in the art would have motivated to modify the method of Oishi98 by detecting the PncA gene because Ramada teaches PCR amplification of DNA is a rapid and reliable method for rapid diagnosis of the presence of a target microorganism, and teaches a method using PCR to detect the PncA gene to identify the presence of M. tuberculosis. One of ordinary skill in the art would have had a reasonable expectation of success because Oishi98 and Ramadan relate to methods of detecting nicotinamidase in a sample.
Therefore, the invention of claims 6-7 and 9 would have been obvious to one of ordinary skill in the art before the effective filing date.
Claim 10 and 14-15 are rejected under 35 U.S.C. 103 as being unpatentable over Oishi98 in view of Ramadan as applied to claims 1, 4-9 and 11-13 above, and further in view of Stacey et al. (Cancer Cell Culture: Methods and Protocols, 2nd Ed, Methods in Molecular Biology, 2011, 731:79; cited on the Form PTO-892 mailed 03/05/2026; herein referred to as Stacey).
The instant rejection is maintained from the previous office action, any newly recited portion is necessitated by claim amendment.
Claim 10 is drawn to the method of claim 1, wherein the sample is a sample from a therapeutic product.
Claim 14 (claim 15 dependent therefrom) is drawn to a method for monitoring bacterial and/or fungal cell contamination in a cell or tissue culture, the method comprising determining the levels of NA and NAA in a cell or tissue culture supernatant sample, wherein an increase in the ratio of NA to NAA levels as compared to a reference indicates bacterial and/or fungal cell contamination in the cell or tissue culture. The teachings of Oishi98 and Ramadan as applied to claims 1, 4-9 and 11-13 are discussed above. These references do not teach the sample is a sample from a therapeutic product.
Stacey relates to cell culture contamination [title], and discusses microbial contamination to be a major issue in cell culture [abstract].
Regarding claim 10, Stacey teaches Mycoplasma as a widespread cause of cell culture contamination [p 82, para 2] whose damaging effects are well known through various reviews [p 83, first paragraph], and teaches that the success rate for complete eradication of Mycoplasma is poor [p 83, para 2]. Stacey further teaches that the immediate response to the detection of a bacterial or fungal contamination should be to discard affected cultures [p 83, Section 6, first paragraph], and that detection of Mycoplasma can be achieved using a number of different methods [p 83, para 2]. As the instant specification does not provide a specific definition for “a therapeutic product”, but gives examples of therapeutic products that include a cell, gene, protein, antibody or vaccine [p 7, final paragraph], the cell culture of Stacey is considered to correspond to the limitation of “a therapeutic product”.
In view of Stacey, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date to modify the combined method of Oishi98 and Ramadan by using a sample from a therapeutic product, as taught by Stacey, to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to modify the combined method of Oishi98 and Ramadan by using a sample from a therapeutic product because Stacey indicates the detection of Mycoplasma contamination in cell culture is important for the prevention of damaging effects associated with such contamination. One of ordinary skill in the art would have had a reasonable expectation of success because both Ramadan and Stacey relate to detection of Mycoplasma in samples.
Regarding claim 14, Oishi98 teaches the detection of increased ratios of NA:NAA in meat samples compared to a corresponding reference that is attributed to nicotinamidase activity corresponding to a bacterial contamination as discussed in the rejection of claim 12 above, Stacey teaches the detection of bacterial contamination in cell culture from Mycoplasma is important to prevent the damaging effects of such contamination as discussed in the rejection of claim 10 above, and Ramadan teaches the detection of Mycoplasma in samples using PCR to identify the presence of the nicotinamidase gene as discussed in the rejection of claim 6 above.
Additionally, Stacey teaches as the actual source of contamination often may not be resolved, and the process of recovery from a contamination incident will clearly demand careful monitoring to insure the original problem does not reappear, which may comprise specific testing [p 85, para 2], which include routine test methods [p 88, col 1]. These teachings are considered to correspond to methods of monitoring bacterial and/or fungal contamination.
Therefore, the combined method of Oishi98, Ramadan and Stacey of monitoring bacterial and/or fungal contamination via detecting nicotinamidase or nicotinamidase activity in a therapeutic product of a cell culture is considered to satisfy the claim 14 limitations of detecting the presence of nicotinamidase or nicotinamidase activity in a cell culture, wherein said presence indicates bacterial contamination of the cell culture.
Regarding claim 15, the instant specification does not set forth a specific definition for “real-time”, and is therefore being examined with the plain definition of an action occurring without delay. In view of this interpretation, the combined method of Oishi98, Ramadan and Stacey of detecting nicotinamidase or nicotinamidase activity from cell cultures is considered to occur in real-time, as the detection is being carried out directly on cell cultures.
Therefore, the invention of claims 10 and 14-15 would have been obvious to one of ordinary skill in the art before the effective filing date.
Response to Remarks: beginning on page 13 of Applicant’s response to rejections under 35 USC 103; Applicant in summary contends Oishi does not teach or suggest methods for determining levels of NA and NAA in the supernatant of a tissue or cell culture sample as recited in the amended claims, as Oishi is instead drawn to detecting nicotinamidase activity in cell extracts of isolated bacteria; Applicant further contends the use of Oishi in the rejection relies on an overly broad generalization that nicotinamidase activity is predictive of NA and/or nicotinamide (NAM) activity, and that Oishi is not capable of the real-time monitoring comprising UV absorbance spectroscopy as recited by the amended claims.
Applicant’s remarks are considered and found not convincing.
Oishi discloses an assay of nicotinamidase activity catalyzing deamidation of NAA to nicotinic acid NA, wherein increases of NA attributed to nicotinamidase activity correspond to the presence of bacteria. Oishi determines levels of NA and NAA as shown in Figure 2. Oishi determines these levels from meat-derived samples, wherein bacterial strains were isolated from meat samples, grown in cell culture media, and thereafter isolated cells were disrupted for the collection of supernatant that was referred to as crude extract, wherein the crude extract was measured for NA and NAA levels as shown in Figure 2. These levels were attributed to bacterial nicotinamidase activity, and therefore indicate the presence of bacteria in a sample. The teachings of Oishi are therefore considered to correspond to a method for detecting levels of NA and NAA in the supernatant of a cell culture sample, and attributing an increase in the ratio of NA:NAA to bacteria cell in the sample.
Additionally it is noted that while the claims recite “wherein an increase in the ratio of nicotinic acid to nicotinamide levels as compared to a reference indicates the presence of a bacterial and/or fungal cell in the tissue or cell culture sample,” this “wherein” clause, while reciting a correlation between the ratio of nicotinic acid to nicotinamide levels as compared to a reference indicates the presence of a bacterial and/or fungal cell in the tissue or cell culture sample, does not require any active step(s) to be performed and given a broadest reasonable interpretation, the “wherein” clause is non-limiting. See MPEP 2111.04. As the claim does not recite an active step of determining an NA:NAA ratio and can be interpreted such that the “wherein clause” is considered to merely recite a correlation between an increase in the ratio and presence of bacterial and/or fungal cells, the teachings of Oishi regarding the recited steps of the method set forth in the rejection above are considered to teach or suggest the claimed method.
Regarding the assertion that the use of Oishi in the rejection relies on an overly broad generalization that nicotinamidase activity is predictive of NA and/or NAM activity: it is unclear how the method of Oishi which detects the presence and levels of NA and NAM (referred to as NAA in the rejection) as used in the rejection would be considered an overly broad generalization, as Oishi detects the two metabolites and directly teaches their abundance to be the result of bacterial nicotinamidase activity. Applicant references the specification para 0028 for features of the invention which are not taught by Oishi, which reads:
[0028] Without being bound by theory, the inventors have found that it is possible to detect broad-based bacterial contamination in cell and gene therapy products (CTPs) with faster speed, smaller product volume and without the need to perform cell or target labelling or cell lysis. The test can be performed without the need of transferring CTPs to certain medium for enrichment and incubation. In addition, other types of detection techniques including ELISA, antibody/nanobody/recombinant protein-based lateral flow assay and optical detection can be developed based on this invention.
However, these features from para 0028 of the specification are not recited in the claims.
Regarding the assertion that the method of Oishi is not capable of real-time monitoring comprising the use of UV-absorption: as noted in the rejection above, Oishi teaches the detection of NA and NAA via UV-absorption. The limitation of performing the method in “real-time” is recited in claim 15, and as the instant specification does not set forth a specific definition for “real-time”, it is considered to have the plain definition of an action occurring without delay. In view of this interpretation, the combined method of Oishi98, Ramadan and Stacey corresponding to claim 15 of detecting nicotinamidase or nicotinamidase activity from cell cultures is considered to occur in “real-time,” as the detection is being carried out directly on cell cultures.
Conclusion
Status of the Application:
Claims 1 and 4-15 are pending.
Claims 1 and 4-15 are rejected.
No claim is in condition for allowance.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH SPANGLER whose telephone number is (571)270-0314. The examiner can normally be reached M-F 7:30 am - 4:30 pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Manjunath Rao can be reached at (571) 272-0939. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/JOSEPH R SPANGLER/
Examiner
Art Unit 1656
/David Steadman/Primary Examiner, Art Unit 1656
Prosecution Insights