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 .
DETAILED ACTION
Claims 3, and 19-26 are cancelled. Claims 1, 2, and 4-18 are pending and under examination.
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 10/14/2025 has been entered.
Response to Arguments
Applicant's arguments filed 10/14/2025 have been fully considered but they are not persuasive. Applicant argues that Huang’s disclosure is not enabling for transforming cells of a biofilm because the Examples in Huang teach the transformation of single colonies. However, Huang explicitly teaches that the process may be used to transform a biofilm (Page 5, Paragraph 4), and teaches introducing DNA to natural microbial communities in order to promote enhanced biodegradation of pollutants in groundwater or wastewater treatment plants, which are considered in situ biofilms. Therefore, there is an expectation of success. Applicant argues that the method of Huang is useful for transforming cells extracted from the biofilm, i.e., the biofilm is broken up prior to transformation. However, nowhere does Huang mention that the cells must be extracted from the biofilm or that the biofilm must be broken up. Applicant only points to parts of the Huang disclosure, such as the examples, that were not relied on for the basis of this rejection.
Applicant’s arguments regarding the Sugano reference are considered moot as said reference is not relied on for the rejection presented in the Office action.
The Declaration of Dr. Wei Huang under 37 CFR 1.132 filed on 10/14/2025 is insufficient to overcome the rejection of claims 1 and 7-17 based upon Huang et al. (GB 2452543) as set forth in the last Office action because: It includes statements which amount to an affirmation that the claimed subject matter functions as it was intended to function. This is not relevant to the issue of nonobviousness of the claimed subject matter and provides no objective evidence thereof. See MPEP § 716. The Declaration discloses that the present invention led to unexpected results, but does not include any comparative experiments to demonstrate that the instant method achieves results that differ from the results achieved by the method of Huang. The Declaration further restates arguments presented in Applicant Arguments/Remarks filed 10/14/2025, but does not provide any evidence that the method of Huang would result in destruction of a biofilm. As stated, Huang explicitly teaches that the method may be used to transform the cells of a biofilm and does not disclose that the cells must be broken up.
The instant specification discloses that the cavitation shockwave is responsible for disrupting the biofilm cell membrane while avoiding disintegration of the biofilm itself (p. 4, lines 10-14). Huang explicitly teaches transformation via ultrasound, and teaches that ultrasound DNA delivery is based on a cavitational effect (Page 2, Paragraph 1). Therefore, it is considered that the method of Huang reads on the limitations of the instant claims, i.e., the method of Huang does not result in destruction of the biofilm. Therefore, Applicant’s arguments are not considered persuasive.
Claim Objections
Claims 12 and 14 are objected to because of the following informalities: the claims contain grammatical errors.
Claim 12 may be amended to recite:
The method according to claim 1, wherein the heterologous nucleic acid is a gene and/or regulatory element of a gene that is involved in one or more functions selected from the group consisting of quorum sensing, cell metabolism, heat/cold resistance, heat-shock resistance, chemical resistance, antibiotic resistance, cell aggregation, cell adhesion, cell export, membrane transportextracellular polymeric substance response, and a combination thereof;
or wherein the heterologous nucleic acid encodes a redox pathway or one or more parts thereof.
Claim 14 may be amended to recite:
The method according to claim 1, wherein the heterologous nucleic acid encodes a protein selected from any of the group consisting of protein-degrading enzymes[[;]], polysaccharide-degrading enzymes,, lipid-degrading enzymes[[;]], phosphomonoesterases[[;]], oxidoreductases[[;]], enzymes, and combinations thereof;
or wherein the heterologous nucleic acid contains one or more genes from the gene cluster mtrCAB or ribADEHC.
Appropriate correction is required.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention 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 35 U.S.C. 103 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1 and 7-17 are rejected under 35 U.S.C. 103 as being unpatentable over Huang et al., (GB 2452543 B), previously cited, as evidenced by Herrling et al., 2019 (Recent NMR/MRI studies of a biofilm), previously cited, and Rao et al., 2010 (Role of enzymes in the remediation of polluted environments), previously cited.
Regarding claim 1, Huang teaches a process for the transformation of host cells with heterologous nucleic acid comprising exposing a mixture of host cells and the nucleic acid to ultrasound frequency (Page 2, Paragraph 5). Huang teaches that ultrasound DNA delivery is based on a cavitational effect (Page 2, Paragraph 1). Huang teaches that the process may be used to transform a biofilm (Page 5, Paragraph 4) which are communities of microorganisms that are embedded in a self-produced extracellular matrix, as evidenced by Herrling et al., 2019 (Introduction, Paragraph 1).
Huang does not ipsis verbis teach in situ biofilm. However, Huang (Page 6, Paragraphs 3 and 4) teaches that efficient transfer of DNA to natural microbial communities, such as those found in groundwater and soils, may be used to rapidly introduce useful gene functions to change the structure and functionality of microbial communities, for example; and teaches introducing DNA to natural microbial communities in order to promote enhanced biodegradation of pollutants in groundwater or wastewater treatment plants. A microbial community found in groundwater, soil, or a wastewater treatment plant is considered in situ, therefore, it would be obvious to one of ordinary skill in the art that an in situ biofilm found in the aforementioned environments are transformed using the methods taught by Huang. Because Huang does not disclose that the method requires destruction of a biofilm, and teaches the active steps of claim 1, transformation without destruction or reconstitution of the biofilm is considered an inherent result of the method of Huang.
Regarding claim 7, Huang teaches that the host cells and heterologous nucleic acid are mixed and exposed to ultrasound frequency for no longer than 60 s (p. 2, para. 5). Therefore, it is it is considered that there is no incubation period between addition of DNA and exposure to ultrasound, i.e., the incubation time of Huang is 0s.
Although this incubation time differs from that of instant claim 7, MPEP 2144.05 II, states: "[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955) (Claimed process which was performed at a temperature between 40°C and 80°C and an acid concentration between 25% and 70% was held to be prima facie obvious over a reference process which differed from the claims only in that the reference process was performed at a temperature of 100°C and an acid concentration of 10%.); see also Peterson, 315 F.3d at 1330, 65 USPQ2d at 1382 ("The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set of percentage ranges is the optimum combination of percentages.")
The selection of an incubation time between the addition of heterologous nucleic acid and ultrasound application would have been a routine matter of optimization and experimentation on the part of the artisan of ordinary skill, and said artisan recognizing that transformation efficiency would have been affected said incubation time.
Regarding claim 8, Huang teaches that efficient transfer of DNA to microbial communities, such as those found in groundwater or soils, may be used to rapidly introduce useful gene functions to change the structure and functionality of microbial communities (Page 6, Paragraph 3). Huang teaches that their invention may be used to transform a biofilm of microorganisms (Page 5, Paragraph 3).
Regarding claim 9, Huang teaches a process for the transformation of host cells with heterologous nucleic acid comprising exposing a mixture of host cells and the nucleic acid to ultrasound frequency (Page 2, Paragraph 5). Huang teaches that ultrasound DNA delivery is based on a cavitational effect (Page 2, Paragraph 1)
Regarding claim 10, Huang teaches that the nucleic acid may be a plasmid (Page 3, Paragraph 3).
Regarding claim 11, Huang teaches that the transformation process may be used to incorporate a marker or genetic trait into the host cells, such as resistance markers or enzymes that digest pollutants (Page 5, Paragraph 4), which would result in a change in host cell phenotype.
Regarding claim 12, Huang teaches that a resistance marker may be incorporated into the genome of the host cell (Page 5, Paragraph 4). Huang specifically teaches that resistance to kanamycin arose as a result of ultrasound DNA delivery (UDD) (Page 13, “Confirmation of plasmid delivery to P. putida UWC1, E. coli DH5α and P. fluoresens SBW25”).
Regarding claim 13, Huang teaches that the host cells may be transformed with a nucleic acid encoding an enzyme (Page 5, Paragraph 4).
Regarding claim 14, Huang teaches that host cells may be transformed with enzymes that digest pollutants. Oxioreductases are the most representative enzymatic classes in the remediation of polluted environments, as evidenced by Rao (Page 336, Column 2, Paragraph 2). Therefore, one of ordinary skill in the art would be reasonably expected to understand that the method of Huang may be used to transform an oxioreductase enzyme that digests pollutants.
Regarding claim 15, Huang teaches that the transformation process may be used to incorporate a marker or genetic trait into the host cells, such as resistance markers or enzymes that digest pollutants (Page 5, Paragraph 4). Therefore, cells of a biofilm transformed with a resistance marker would have enhanced survival and/or growth relative to species not transformed with said resistance marker.
Regarding claim 16, Huang teaches the addition of CaCl2 to DNA transfer media to enhance ultrasound DNA delivery (Page 14, Paragraph 1).
Regarding claim 17, Huang teaches a process for the transformation of host cells with heterologous nucleic acid comprising exposing a mixture of host cells and the nucleic acid to ultrasound frequency (Page 2, Paragraph 5). Huang teaches that ultrasound DNA delivery is based on a cavitational effect (Page 2, Paragraph 1). Huang teaches that the process may be used to transform a biofilm (Page 5, Paragraph 4) which are communities of microorganisms that are embedded in a self-produced extracellular matrix, as evidenced by Herrling et al., 2019 (Introduction, Paragraph 1). Huang teaches that the transformation process may be used to incorporate a marker or genetic trait into the host cells, such as resistance markers or enzymes that digest pollutants (Page 5, Paragraph 4), which would modify the host cell phenotype. Because Huang teaches the active steps of claim 17, transformation without destruction or reconstitution of the biofilm is considered an inherent result of the method of Huang.
Claim 2 is rejected under 35 U.S.C. 103 as being unpatentable over Huang et al., (GB 2452543 B) as applied to claim 1 above, and further in view of Frohly et al., 2000 (Ultrasonic cavitation monitoring by acoustic noise power measurement), previously cited.
Huang teaches a method of transforming biofilms in situ using ultrasound-induced cavitation.
Huang does not teach monitoring of inertial cavitation by acoustic cavitation noise.
However, Frohly teaches a method of monitoring acoustic cavitation (Abstract).
It would have been obvious to one of ordinary skill in the art, prior to the effective filing date of the claimed invention, to have monitored inertial cavitation taught by Huang via acoustic cavitation noise as taught by Frohly. One of ordinary skill in the art would have been motivated to do so because Frohly teaches that acoustic cavitation noise is a suitable and accurate indicator of the cavitation activity induced in a liquid (Abstract). One of ordinary skill in the art would have had a reasonable expectation of success because Huang and Frohly are in the same field of endeavor of ultrasonic cavitation studies.
Claims 4-6 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Huang et al., (GB 2452543 B), as applied to claim 1 and 17 above, and further in view of Scholz et al., 1990 (A two-compartment cell entrapment bioreactor with three different holding times for cells, high and low molecular weight compounds), previously cited.
Huang teaches a method of transforming the cells of a biofilm -in situ, but does not teach the use of an enclosure.
However, regarding claims 4 and 18, Scholz teaches a bioreactor for cell cultivation (Abstract). It is interpreted that the bioreactor comprising the cells is considered an “enclosure”.
Regarding claim 5, Scholz teaches that the bioreactor has a sampling port for the injection of materials (Page 133, Column 2).
Regarding claim 6, Scholz teaches that the bioreactor contains two compartments, for cells and medium, respectively. Scholz teaches that the chambers are separated by an ultrafiltration membrane (Abstract). Scholz teaches that the cells are retained in the reactor and the high molecular weight products accumulate in the cell chamber, while the small molecular weight nutrients and metabolites are replenished and removed from the medium chamber (Abstract) and that low molecular weight nutrients freely diffuse to and from the cell chamber (Page 129, Column 1). Therefore, it is interpreted that the second compartment of Scholz may be used to retain and release substances into the first compartment containing cells.
It would have been obvious to one of ordinary skill in the art, prior to the effective filing date of the claimed invention, to have utilized an enclosure as taught by Scholz to deliver heterologous nucleic acid to cells as taught by Huang. One of ordinary skill in the art would have been motivated to do so because Scholz teaches that, by adjusting the flow rates for cell and medium chambers, the resident time for cells, high, and low molecular weight components can be manipulated separately (Abstract). One of ordinary skill in the art would have had a reasonable expectation of success because Huang and Scholz are in the same field of endeavor of cell culture methods.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RACHEL EMILY MARTIN whose telephone number is (703)756-1416. The examiner can normally be reached M-Th 8:30-16:00, F 8:30-10:00 EST.
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/RACHEL EMILY MARTIN/Examiner, Art Unit 1657