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 .
Election/Restriction Requirement
Applicant’s election SEQ ID NO: 47 for the species. This species is a for binding H1N1 virus so reads on claims 1-3 and 6-19 in the reply filed on 1/30/17 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)). Claims 4, 5 and 20 are withdrawn as non-elected species. Claim 20 was a non-elected invention from the restriction on 7/8/25.
Claim Interpretation
The claims are drawn to a material which comprises a genetically modified microbial cells comprising a fusion protein of amyloid domain and a binding domain operative to bind a contaminant. The phrase contaminate is broad since it reads on any chemical compound other water in an aqueous solution. Art reading on binding a specific compound limited in the claims will read as binding to the contaminant. Also the phrase “thereby facilitate the decontamination of the water source” is a wherein clause that limits the result when composition is used. MPEP 2112.01 I and II are clear that if the prior art teaches a structure that is physically the same or similar, then its properties and functions are presumed to be the same as those claimed. Therefore art reading on the structure of the biofilm will also read on these intended results.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 2, 8 and 10-12 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding claims 2 and 10-12 , the phrase "e.g." renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d). In the interest of compact prosecution only the Genus listed outside of the parenthesis will be considered.
Claim 8 also is confusing because of the combination of the amyloid gene with a bacterial species in parenthesis (e.g. “TasA (B.subtilis)”). It is unclear how the bacterial species modifies the gene. If the Applicant wishes the gene from a specific source they might wish to amend to “TasA gene from B. subtilis”.
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)(1) 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.
Claim(s) 1, 8-13 are is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Joshi et al. (WO 2014/176311).
Joshi et al. teach biofilms of E. coli genetically modified with a fusion protein of a CsgA amyloid and a peptide binding domain (Figs. 8, and 16As) for wastewater treatment [00238]. The fusion proteins self-assembles on the surface of the bacteria where the binding domain captures its target molecule. Table 1 shows the various peptide biding domains fused to the CsgA that can bind to various substrates [0026 and 00253]. Fig. 18 shows the biofilms with the fusion protein CsgA-A3 can bind to AgNO3 contaminants in an aqueous solution (e.g. a water source) [0026 and 00261].
Therefore the invention as a whole is anticipated by the reference.
Claim(s) 1, 8, 10-19 are is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Huang et al. (Nature Chemical Biology 2018).
Huang et al. teach a bacterial biofilm of B. subtilis genetically engineered to produce a fusion protein of TasA amyloid and a binding domain expressed on the surface of the bacteria (Fig 1). These biofilms bind specific contaminants in water including organophosphates (Fig. 2 and Fig. 3d). These biofilms can be cultured on various industrial 3D-printed hydrogel fillers (Fig 4 and Fig 5). The biofilm colonizes this industrial filler to make a water decontamination system.
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.
Claim(s) 1-3, and 6-13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Joshi et al. (WO 2014/176311) in view of Matsubara et al. (Frontiers in Microbiology, 2016) and Vidakovic et al. (Nat Microbiol 2018).
Joshi et al. teach biofilms of E. coli genetically modified with a fusion protein of a CsgA amyloid and a peptide binding domain (Figs. 8, and 16As) for wastewater treatment and removal of contaminants from groundwater [00238]. The fusion proteins self-assembles on the surface of the bacteria where the binding domain captures its target molecule. Table 1 shows the various peptide biding domains fused to the CsgA that can bind to various substrates [0026 and 00253] including other protein and inorganic substrates. Fig. 18 shows the biofilms with the fusion protein CsgA-A3 can bind to AgNO3 as a contaminant in an aqueous solution (e.g. a water source) [0026 and 00261].
Joshi et al. does not teach a specific binding domain of SEQ ID NO:47 which binds to H1N1 influenza virus. This would be obvious in view of Vidakovic et al. and Matsubara et al. Vidakovic et al. teach CsgA fibers in E. coli binds virus phage particles (Vidakovic, Abstract and pg. 4 top). Matsubara et al. teach that HA-binding peptide (Ala-Arg-Leu-Pro-Arg, SEQ ID NO: 47) that specifically binds H1N1 virus.
One of ordinary skill in the art would recognize it obvious to modify Joshi et al. by adding the HA binding peptide to a fusion protein with CsgA fibers. Vidakovic et al. already teach that CsgA fibers on E. coli biofilms bind viruses. Matsubara et al. teach the HA-binding peptide is specific to H1N1 virus. One of ordinary skill would recognize that adding the HA-binding peptide to the CsgA-fusion protein in Joshi et al. would produce an E. coli biofilm that would selectively capture H1N1 which could be used to remove this virus from wastewater and groundwater. One of ordinary skill would recognize that removing H1N1 from wastewater and groundwater would reduce the spread of H1N1. One of ordinary skill would recognize this as simply applying a different binding agent to the CsgA-fusion protein would improve the invention of Joshi et al. by allowing it to capture viruses from water. One of ordinary skill would recognize this as simply applying a known binding agent to H1N1 to a fusion protein to bind additional components in waste or ground water (MPEP 2141 V (C, D, F)).
Therefore the invention as a whole would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made, as evidenced by the references, especially in the absence of evidence to the contrary.
Claim(s) 1, 8-19 are is/are rejected under 35 U.S.C. 103 as being unpatentable over Joshi et al. (WO 2014/176311) in view of Lewandowski et al. (Biofilms in Water and Wastewater Treatment, 2011).
Joshi et al. teach biofilms of E. coli genetically modified with a fusion protein of a CsgA amyloid and a peptide binding domain (Figs. 8, and 16As) for wastewater treatment and removal of contaminants from groundwater [00238]. The fusion proteins self-assembles on the surface of the bacteria where the binding domain captures its target molecule. Table 1 shows the various peptide biding domains fused to the CsgA that can bind to various substrates [0026 and 00253] including other protein and inorganic substrates. Fig. 18 shows the biofilms with the fusion protein CsgA-A3 can bind to AgNO3 contaminates in an aqueous solution (e.g. a water source) [0026 and 00261].
Joshi et al. does not teach their biofilms to treat wastewater or ground water are cultured on industrial filler. However this would be obvious in view of Lewandowski et al. who teach a variety of biofilm fillers or carriers (Lewandowski, pg. 552, Table 2) to culture and adhere the biofilm for use in industrial wastewater treatment reactors. One of ordinary skill would recognize it as obvious to use the industrial fillers of Lewandowski et al. for the biofilms of Joshi et al. since both are drawn to treating wastewater with biofilms (MPEP 2141 (C-D)).
Therefore the invention as a whole would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made, as evidenced by the references, especially in the absence of evidence to the contrary.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-4, 8, 10-12 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-5 of U.S. Patent No. US 11,365,224. Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are drawn to genetically engineered Bacillus subtilis biofilms comprising:
Expresses a recombinant fusion protein comprising TasA and a binding domain; and
The binding domain comprises organophosphate hydrolase that binds organophosphates including the pharmaceutical paraoxon (a cholinesterase inhibitor).
In response to this office action the applicant should specifically point out the support for any amendments made to the disclosure, including the claims (MPEP 714.02 and 2163.06).
CONTACT INFORMATION
Any inquiry concerning this communication or earlier communications from the examiner should be directed to THANE E UNDERDAHL whose telephone number is (303) 297-4299. The examiner can normally be reached Monday through Thursday, M-F 8-5 MST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Fereydoun Sajjadi can be reached at (571) 272-3311.The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/THANE UNDERDAHL/Primary Examiner, Art Unit 1699
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