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 .
Claim status
Claims 1-21, are pending. Claims 1-21, are examined in the instant application.
Priority
This application is claiming the benefit of Provisional Application No.
63/438,072 filed 01/10/2023.
Information Disclosure Statement
Initialed and dated copy of Applicant’s information disclosure statement (IDS) filed on 07/09/2025, 07/09/2025, and 08/27/2025 are attached to the instant Office Action. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Drawings
The drawings are objected to because:
Figure 19A, is unclear because the symbols are unreadable and one cannot distinguish between treatments.
Figure 22A, is unclear which line is for tomato and which line is for cabbage.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claims 6, 8, and 10 are objected to because of the following:
In regard to claim 6, “dnaA, gyrA, polA, or ftsZ” should be spelled out the first time using it.
In regard to claim 8, “oriV” should be spelled out the first time using it. Also “oriV” need to be italicized.
Appropriate correction is required.
Specification
The disclosure is objected to because of the following:
In page 44, table 9, the recitation of “gRNA_5 is a Non-coding region” is incorrect. According to the specification table 7 states that it is a “pR.036 CRISPR-gRNA 5 pCym-cas9-gRNA5 (polA Xcc) RK2 par locus” and seems to be an error. Does Applicant mean to say “polA”?
Claim Rejections - 35 USC § 112 (Indefinite)
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, 3 and 19-20 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.
In regard to claims 2-3, the recitation “90% sequence identity” is unclear. How is one skilled in the art supposed to know percent identity to sequence/structure when no sequence identifier is recited?
In regard to claim 3, the recitation of “less than 90% sequence identity to a sequence in a bacterial species other than that of the one or more species of plant-associated bacteria” is unclear because claim 2 recites “at least 90% sequence identity to the sequence in the genome of one or more species of plant-associated bacteria” so that the guide sequences would fall in between both above and below 90%. Would they be targeted or not? Would the gene create off-target effects because of how close sequence identity is to the gene?
In regard to claims 19-20, is the “domain essential to the replication” the same as “origin of replication” in claim 1, line 11? Or is it a gene that aids in replication? Additionally, the recitation of “genome modification” is unclear.
Moreover, the claim is indefinite because it is not clear how the modified bacteria further comprises a “genome” modification comprising a domain essential to the replication of the vectors as the vectors are heterologous to the modified bacteria and thus do not have any domains essential to replication in the bacterial genome.
Claim Rejections - 35 USC § 112(a)(Written Description)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-21, are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Applicant’s disclosure is as follows.
Applicant described engineering a bacterial expression system that comprises two expression vectors, wherein the 1st vector comprises the target gene, and the 2nd vector comprises pTAmob conjugative plasmid as the bacterial conjugation machinery (ex 18). The specification describes the killing efficiency in Xanthomonas campestris, Xanthomonas perforans, Xanthomonas euvesicatoria, and Erwinia amylovora utilizing the target genes dnaA (SEQ ID NOs:53-54 and 88), polA (SEQ ID NO: 71), fitZ (SEQ ID NOs: 72 and 79), and gyrA (SEQ ID NOs: 81 and 89), which all the constructs had high killing efficiency (fig. 6).
Additionally, the specification describes that co-transforming Pseudomonas putida with pTAmob and the Cas9-gRNA plasmid pR.036 designed to target X. campestris and a panel of five non-target bacteria (X perforans, X. euvesicatoria, E. coli, P. syringae, and P. protegens) (ex. 20) resulting in little to no off-target effects and 99.7% efficiency in the target species of X. campestris (fig. 9). Lastly, the specification described significantly reducing disease symptoms and having high bacterial killing efficiency in tomato, lettuce, apple, and citrus (exs. 23-37).
Claim 1 is directed to a bacterial expression vector system comprising 2 expression vectors. The claim is open to a first expression vector comprising gRNA that targets any and all sequences in one or more plant-associated bacteria (PAB) and a second vector comprising nucleic acids encoding for ad infinitum bacterial conjugation machinery.
However, the specification does not adequately describe a representative number of gRNA that targets sequences in the genome of a PAB or sequences encoding for bacterial conjugation machinery.
Therefore, due to the lack of written description one skilled in the art would find it hard to believe that the Applicant is in possession of the genus of guide nucleic acids targeting one or more sequences in the genome of a PAB as claimed or possesses the structures of bacterial conjugation machinery as broadly claimed.
For example, Hamilton et al . (Nat. Commun., Vol. 10, Article 4544, 2019, https://doi.org/10.1038/s41467-019-12448-3. (U)), describes that over 60 essential and non-essential genes are targeted using guide nucleic acid, yet killing efficiencies ranged from 1-100% with colonies capable of escaping killing (p. 4, col. 2).
Hamilton et al. describes that a robust understanding of parameters that influence sgRNA (i.e., guide nucleic acids as claimed) targeting and activity in prokaryotic genomes remains a work in progress (p. 4, col. 2 spanning p. 5). This demonstrates that bacterial conjugation targeting sequences in a genome of a recipient bacteria do not function as predicted.
Additionally, the claims fail to describe the structural elements necessary to prevent the engineered gRNA from targeting endogenous host gene prior to transfer. Without these features, the carrier bacteria would undergo self-targeting and die before conjugative transfer to the targeted pathogen can occur, rendering the claimed inventions unable to practice as broadly written.
With respect to claims 2-3, the specification does not actually describe a representative number of structures from the genus of guide nucleic acids comprising at least 90% sequence identity to a sequence in the genome of a PAB. This is necessary because Hamilton et al. describe that bacterial conjugation targeting sequences in a genome of a recipient bacteria do not function as predicted.
The specification does not provide a representative number of structures having at least 90% sequence identity to the sequence in the genome of one or more species of PAB.
Claim 3 encompasses guide nucleic acids that comprises less than 90% sequence identity to an undisclosed sequence in all bacteria species. How is one skilled in the art supposed to distinguish between what is the target gene and what is not the target gene. For example, if the target gene was housekeeping gene which is conserved within all bacterial species would the 90% sequence identity encompass all genes.
In regard to claim 5, is directed to a gene in the genome of one or more species of plant-associated bacteria is in a region of an essential gene is not adequately described. The specification does not describe a representative number of regions in essential genes. The specification has not described whether the essential gene is also essential in both beneficial and harmful bacteria. For example, the claim lacks the necessary structural limitation to prevent self-targeting or non-target PAB’s resulting in death before the host genes transfer target genes.
In regard to claim 6, the specification does not describe if the guide nucleic acids targeting essential genes dnaA, gyrA, polA, or ftsZ, would also target the modified bacteria responsible for conjugation. For example, Hansen et al. (Frontiers in microbiology, vol. 9, issue 319. 28 Feb. 2018, doi:10.3389/fmicb.2018.00319 (V)) describes that “virtually all bacteria have DnaA proteins that interacts with DnaA boxes to initiate chromosome replication” (Abstract). Therefore, the specification fails to describe that the first vector doesn’t also target the bacteria carrying and transferring each of the vectors.
Claim 11 is directed to the TrfA of the second expression vector, not the TrfA of the first expression vector. While one skilled in the art can generate a population of sequences having 80-99.5% sequence identity to SEQ ID NO:46, one skilled in the art cannot predict which sequence(s) within said population would confer a functional TrfA gene. Neither the state of the prior art nor Applicant’s disclosure describes regions within SEQ ID NO:46 that must be conserved for a functional TrfA protein. Accordingly, TrfA proteins comprising 80-99.5% sequence identity to SEQ ID NO:46.
Moreover, while one skilled in the art can generate a population of sequences having at least 80% identity to SEQ ID NO: 46. This requires the specification to describe said amino acid sequences. However, the specification does not describe an amino acid sequence having at least 80% identity to SEQ ID NO: 46, which leads to a functional TrfA vector construct.
An amino acid sequence having at least 80% identity to SEQ ID NO: 46 would have 77 amino acid substitutions relative to SEQ ID NO: 46. These polypeptide would encompass 1977 distinct protein variants. In the absence of describing where in the sequence of SEQ ID NO:46 such variations can be sustained, one of skill in the art would not be led to believe that Applicant possesses this vast genus of claimed polypeptide of SEQ ID NO: 46, and lead to producing a functional construct let alone a polypeptide sequence having at least 80% sequence identity of SEQ ID NO: 46.
Claims 12-13 are directed to targeting a sequence in a non-essential gene or non-coding region of one or more PAB, but the specification fails to disclose any specific sequence, structures, or representative species for these regions. Consequently, the specification lacks written description for the full scope of claimed non-essential and non-coding target regions across the recited PAB species.
Claim 20 is directed to the pirA gene. While one skilled in the art can generate a population of sequences having 80-99.5% sequence identity to SEQ ID NO:49, one skilled in the art cannot predict which sequence(s) within said population would confer a functional pirA gene. Neither the state of the prior art nor Applicant’s disclosure teaches regions within SEQ ID NO:49 that must be conserved for a functional pirA gene. Accordingly, pirA genes comprising 80-99.5% sequence identity to SEQ ID NO:49.
Moreover, while one skilled in the art can generate a population of sequences having at least 80% identity to SEQ ID NO: 49. This requires the specification to describe said nucleic acid sequences.
However, the specification does not describe a nucleic acid sequence having at least 80% identity to SEQ ID NO: 49, which leads to a functional pirA vector construct.
A nucleic acid sequence having at least 80% identity to SEQ ID NO: 49 would have 184 nucleic acid substitutions relative to SEQ ID NO: 49.
These polynucleotide would encompass 3184 distinct gene variants. In the absence of describing where in the sequence of SEQ ID NO:49 such variations can be sustained, one of skill in the art would not be led to believe that Applicant possesses this vast genus of claimed polynucleotide of SEQ ID NO: 49, and lead to producing a functional construct let alone a polynucleotide sequence having at least 80% sequence identity of SEQ ID NO: 49.
Claim 21 is directed to a method of horizontal gene transfer (HGT), but the specification fails to describe the specific structural elements, transfer machinery, or necessary vector (such as conjugative or transfer plasmid) required to achieve HGT across the PAB species. Therefore, one skilled in the art would find it hard to believe the Applicant was in possession of the full scope of the claimed HGT method at the time of filing.
Accordingly, there is lack of adequate description to inform a skilled artisan that Applicant was in possession of the claimed invention at the time of filing. See Written Description guidelines published in Federal Register/ Vol.66, No. 4/ Friday, January 5, 2001/ Notices; p. 1099-1111.
Claim Rejections - 35 USC § 112 (Enablement)
Claims 1-21 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Enablement factors to consider include:
(A) The breadth of the claims;
(B) The nature of the invention;
(C) The state of the prior art;
(D) The level of one of ordinary skill;
(E) The level of predictability in the art;
(F) The amount of direction provided by the inventor;
(G) The existence of working examples; and
(H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. In re Wands, 858 F.2d 731,737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988).
Applicant’s disclosure is as set forth above. The claimed invention is not enabled for the following reasons.
(A) The breadth of the claims;
The breadth of the claims encompasses a bacterial expression system comprising two vectors, wherein the 1st expression comprises gRNA targeting an undisclosed gene in the genome of one or more plant-associated bacteria (PAB), and wherein the 2nd vector comprises, an undisclosed bacterial conjugation machinery, wherein both expression vectors result in low copy origin replication.
(B) The nature of the invention;
The nature of the claimed invention is a bacterial expression system comprising two vectors, wherein the 1st expression comprises gRNA targeting a dnaA, polA, fitZ, and/or gyrA gene in the genome of one or more PAB, and wherein the 2nd vector comprises, an TAmob conjugation plasmid wherein both expression vectors result in low copy origin replication.
(C) The state of the prior art;
The state of the prior art does not teach guide nucleic acids having at least 90% sequence identity to target sequences in the genome of a PAB retain function. The state of the prior art does not teach if sequences having at least 80% sequence identity to TrfA SEQ ID NO: 46 in the 2nd vector will confer functionality, let alone the TrfA from the 1st vector where the structure is not disclosed. The state of the prior art does not teach if sequences having at least 80% sequence identity to pirA SEQ ID NO: 49 will confer functionality.
This guidance is critical because Hamilton et al. teaches that over 60 essential and non-essential genes are targeted using guide nucleic acid, yet killing efficiencies ranged from 1-100% with colonies capable of escaping killing (p. 4, col. 2).
Hamilton et al. teaches that a robust understanding of parameters that influence sgRNA (i.e., guide nucleic acids as claimed) targeting and activity in prokaryotic genomes remains a work in progress (p. 4, col. 2 spanning p. 5). This demonstrates that bacterial conjugation targeting sequences in a genome of a recipient bacteria do not function as predicted.
(D) The level of one of ordinary skill;
The level of one ordinary skill in the art is high.
(E) The level of predictability in the art
It is unpredictable what sequence structure(s) within the 90% sequence identity to an undisclosed sequence in the genome resulting in a functional construct. It is also unpredictable what sequence structure(s) within the 80% sequence identity to TrfA SEQ ID NO: 46 in the 2nd vector will confer functionality, let alone the TrfA from the 1st vector where the structure is not disclosed. It is also unpredictable what sequence structure(s) within the 80% sequence identity to pirA SEQ ID NO: 49 will confer functionality.
(F) The amount of direction provided by the inventor
The specification does not provide guidance as to what structures would result in a functional construct in claim 1. The specification does not provide guidance if 90% sequence identity to an undisclosed sequence in the genome results in a functional construct that targets the sequence. The specification does not provide guidance if 80% sequence identity to TrfA SEQ ID NO: 46 in the 2nd vector will confer functionality, let alone the TrfA from the 1st vector where the structure is not disclosed. The specification does not provide guidance if sequence structure(s) within the 80% sequence identity to pirA SEQ ID NO: 49 will confer functionality.
(G) The existence of working examples
Applicant has no working example of a sequence having 90% sequence identity to an undisclosed target sequence in the genome resulting in a functional construct. Applicant has no working example of a sequence having 80% sequence identity to TrfA SEQ ID NO: 46 in the 2nd vector will confer functionality, let alone the TrfA from the 1st vector where the structure is not disclosed. Applicant has no working example of a sequence having 80% sequence identity to pirA SEQ ID NO: 49 will confer functionality.
(H) The quantity of experimentation needed to make or use the invention
There is not enough guidance or working examples for one skilled in the art to make this construct where at least one guide nucleic acid targets an ad infinitum number of sequences in the genome of a PAB. This guidance is important in light of the unpredictably in using bacterial conjugation machinery as taught by Hamilton et al. and discussed above.
Additionally, the term PAB encompasses all types of bacteria (beneficial, neutral, and harmful). The specification teaches targeting harmful bacteria; however, the specification does not teach or provide guidance for targeting beneficial or neutral bacteria. If the intention of this expression vector is to target harmful bacteria, the specification fails to teach this may be done without off-target effects or unintended consequences. Therefore, it would require undue experimentation to identify the guide nucleic acid sequences and targets in the genome of a PAB.
In regard to claim 2 while one skilled in the art can generate a first expression vector comprising a guide sequence having at least 90% sequence identity to any sequence in the genome, one skilled in the art would not predictably make and use said expression vector. Therefore, it would require undue experimentation to make and use the sequence having at least 90% sequence identity to an undisclosed sequence.
In regard to claims 11 and 20, 80% sequence identity to SEQ ID NOs: 46 and 49 encompasses deletions, additions, substitutions, and any combination thereof anywhere within SEQ ID NOs: 46 and 49. Applicant provides no guidance as to which region(s) of SEQ ID NOs: 46 and 49 can be mutated and which regions(s) of SEQ ID NOs: 46 and 49 must be conserved for functional activity.
While one skilled in the art can make mutations to SEQ ID NOs: 46 and 49, further guidance is needed to readily identify operable embodiments, or readily eliminate inoperable embodiments, without resorting to random trial and error requiring undue experimentation. To require one skilled in the art to make each sequence mutation within said 80% sequence identity, introduce each sequence into a bacteria cell, and incubated with millions of bacteria and test each mutated sequence for functional activity would not be routine experimentation.
Similarly, with regard to claim 9, while one skilled in the art can readily mutate (include additions, substitutions, deletions), TrfA protein, one skilled in the art cannot readily mutate a domain without undue experimentation and location of desired modification. It would require undue experimentation to determine the location of the mutation, without further guidance. The breadth of "mutated" encompasses additions, deletions, substitutions and any combination thereof within the TrfA protein. From this virtually ad infinitum population of sequences, no guidance is provided as to how one skilled in the art can readily identify the desired or operable embodiments or readily eliminate inoperable embodiments without resorting to random trial and error requiring undue experimentation.
Claim 16 is directed to plant pathogenic bacteria, however the specification fails to provide guidance of said pathogenic bacteria or the target genes both essential and non-essential. The lack of working examples in all pathogenic bacteria, would not enable one skilled in the art to make and use said vector. The large genus of plant pathogenic bacteria would make it unpredictable to determine which species of bacteria said vector would function, especially since no specific target gene is disclosed.
Lastly, the claims broadly covers a bacterial expression system comprising two vectors: a first vector with a guideRNA targeting a PAB gene, and a second vector with bacterial conjugation machinery. While the claims encompasses any function, such as increasing bacterial pathogenicity or targeting a silent genes. The specification has only taught on killing pathogenic bacteria. Therefore, the specification fails to enable the full scope of non-killing phenotypes and functions.
Given the breadth of the claim, the state of the prior art, the lack of predictability, and the lack of guidance and working examples, notwithstanding a relatively high level of ordinary skill of those in the art, the amount of experimentation required to make the claimed invention would likely be extensive and undue.
Accordingly, weighing all the Wands factors based on the totality of the record as discussed above, the Office determines that it would require undue experimentation for a person of ordinary skill in the art to make and use the invention as claimed.
Claim Rejections - 35 USC § 102
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 (i.e., changing from AIA to pre-AIA ) 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.
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.
(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.
Claims 1-5, 7-8, 14, 17 and 19 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ruotsalainen et al., (Gut Microbes, Vol.10, NO.6, Pgs.643-653, DOI: 10.1080/19490976.2019.1591136, 2019 (W)).
It is noted that in paragraph 0071 the specification defines PAB as:
bacteria found in any interior or exterior region of the plant. In some embodiments, plant-associated bacteria are found in the phyllosphere, the rhizosphere, the root system, the shoot system, the flowers, the leaves, the fruit, the stem, or the roots. Plant-associated bacteria, as used herein, include bacteria found in any layer of soil that will affect the growth or productivity of a plant. In some embodiments, a plant-associated bacteria is found in the humus layer, the topsoil layer, the eluviation layer, or the subsoil layer.
Therefore, a PAB is considered any bacteria whatsoever including those that are found in or around a plants tissue or ecosystem.
In regard to claims 1, 8, 14 and 17, Ruotsalainen et al. discloses modifying a bacteria comprising two vectors, wherein the first vector comprises guide nucleic acid targeting CRISPR Cas9 blaTEM-52b gene of a PAB, specifically Escherichia coli strain which is found in manure, soil and leaf surface (pg. 645, col. 1, last para.), and wherein the second vector comprises an exogenous nucleic acid that encodes for a bacterial conjugation machinery, conjugative RP4 plasmid (known to have a low copy number origin of replication) (pg. 648, col. 1, last para. and fig. 1a). Through Applicants own admission oriV is derived from RP4 (p. 86, para. [00160]), therefore, Ruotsalainen et al’s. plasmid inherently comprises oriV.
In regard to claims 2 and 4, the claim is not limited to a specific gene, therefore Ruotsalainen et al. discloses at least 90-100% sequence identity to the sequence in the genome of one or more species of PAB.
In regard to claims 3 and 19, Ruotsalainen et al. discloses less than 90% sequence identity to the guide nucleic acid, specifically disclosing a “543 bp region, including the target site of the CRISPR/Cas9 system, was deleted from the beta-lactamase gene blaTEM-2 of RP4 to prevent the system from self-targeting” (p.645, col.1, 2nd para.).
In regard to claim 5, Ruotsalainen et al. discloses targeting an essential antibiotic resistance gene beta-lactamase (p.645, col.1, 2nd para.).
In regard to claim 7, Ruotsalainen et al. discloses that the first expression vector has not been shown to spread (i.e. replicate autonomously) (p.648, col.1 2nd para.).
Therefore, the claimed invention is anticipated by the prior art.
Claim Rejections - 35 USC § 103
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 (i.e., changing from AIA to pre-AIA ) 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.
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 1-5, 7-8, 14-17, 19 and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Ruotsalainen et al., (Gut Microbes, Vol.10, NO.6, Pgs.643-653, DOI: 10.1080/19490976.2019.1591136, 2019 (W)) in view of Bonaterra et al. (Microorganisms, vol. 10, No.9 1759. 31 Aug. 2022, doi:10.3390/microorganisms10091759 (X).
In regard to claims 1,8, 14 and 17, Ruotsalainen et al. teach modifying a bacteria comprising two vectors, wherein the first vector comprises guide nucleic acid targeting CRISPR Cas9 blaTEM-52b gene of a PAB, specifically Escherichia coli strain which is found in manure, soil and leaf surface (pg. 645, col. 1, last para.), and wherein the second vector comprises an exogenous nucleic acid that encodes for a bacterial conjugation machinery, conjugative RP4 plasmid (known to have a low copy number origin of replication) (pg. 648, col. 1, last para. and fig. 1a). Through Applicants own admission oriV is derived from RP4 (p. 86, para. [00160]), therefore, Ruotsalainen et al’s. plasmid inherently comprises oriV.
In regard to claims 2 and 4, the claim is not limited to a specific gene, therefore Ruotsalainen et al. teaches at least 90-100% sequence identity to the sequence in the genome of one or more species of PAB.
In regard to claims 3 and 19, Ruotsalainen et al. teaches less than 90% sequence identity to the guide nucleic acid, specifically disclosing a “543 bp region, including the target site of the CRISPR/Cas9 system, was deleted from the beta-lactamase gene blaTEM-2 of RP4 to prevent the system from self-targeting” (p.645, col.1, 2nd para.).
In regard to claim 5, Ruotsalainen et al. teaches targeting an essential antibiotic resistance gene beta-lactamase (p.645, col.1, 2nd para.).
In regard to claim 7, Ruotsalainen et al. teaches that the first expression vector has not been shown to spread (i.e. replicate autonomously) (p.648, col.1 2nd para.).
In the event that E. coli is not considered a PAB in light of the Office’s interpretation, then Ruotsalainen et al. does not specifically teach on PAB’s, plant bacteria, or plant pathogenic bacteria.
In regard to claims 15-16, Bonaterra et al. teach on the use of Bacillus spp. as bacterial biocontrol agents to control plant disease (Title), specifically that “Bacillus spp. have great potential to control infection through direct inhibition of pathogen growth via antibiosis and/or by interfering with pathogen fitness” (p. 15, sec. 5, 1st sentence).
Therefore, prior to the effective filing date of the instant invention it would have been prima facie obvious to one of ordinary skill in the art to modify the teachings of Ruotsalainen et al. by substituting E. coli for a plant bacterial pathogen species because Bonaterra et al. teaches utilizing bacteria as a biocontrol for bacterial plant diseases. One would have a reasonable expectation of success in doing so because each of Ruotsalainen et al. and Bonaterra et al. teach that is the known practice to utilize bacteria as a biocontrol against bacterial diseases.
Therefore, the claimed invention is obvious over the prior art.
Claim(s) 1, 6 and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Ruotsalainen et al., (Gut Microbes, Vol.10, NO.6, Pgs.643-653, DOI: 10.1080/19490976.2019.1591136, 2019 (W)) and Bonaterra et al. (Microorganisms, vol. 10, No.9 1759. 31 Aug. 2022, doi:10.3390/microorganisms10091759 (X) as applied to claims 1, and 5 above, and further in view of Hamilton et al., (Nat. Commun., Vol. 10, Article 4544, 2019, https://doi.org/10.1038/s41467-019-12448-3.(U))
The teaching of Ruotsalainen et al. and Bonaterra et al. have been discussed above.
Ruotsalainen et al. and Bonaterra et al. do not teach on targeting essential genes dnaA, gyrA, polA, or fitz, or on non-essential genes.
In regard to claims 6 and 12, Hamilton et al. teaches targeting essential genes (i.e. polA) and non-essential genes (fig.3).
Therefore, prior to the effective filing date of the instant invention it would have been prima facie obvious to one of ordinary skill in the art to modify the teachings of Ruotsalainen et al. and Bonaterra et al. by substituting the target gene polA or non-essential genes because Hamilton et al. teaches this leads to a high killing efficiency. One would have a reasonable expectation of success in doing so because each of Ruotsalainen et al. and Hamilton et al. teach the successful application of modifying bacteria to transfer DNA to recipient bacteria to kill it.
Therefore, the claimed invention is obvious over the prior art.
Claims 1, 10 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Ruotsalainen et al., (Gut Microbes, Vol.10, NO.6, Pgs.643-653, DOI: 10.1080/19490976.2019.1591136, 2019 (W)) and Bonaterra et al. (Microorganisms, vol. 10, No.9 1759. 31 Aug. 2022, doi:10.3390/microorganisms10091759 (X) as applied to claims 1, 7 and 17 above, and further in view of Strand et al., (PLoS ONE, Vol. 9(3): e90372, 2014, https://doi.org/10.1371/journal.pone.0090372 (Y) .
The teaching of Ruotsalainen et al. and of Bonaterra et al. have been discussed above.
Ruotsalainen et al. and of Bonaterra et al. do not teach on utilizing plasmid replication initiator protein (TrfA) in the conjugative vector and wherein the second plasmid is a conjugative TAmob plasmid.
In regard to claims 10 and 18, Strand et al. teach on mobilization plasmid pTAmob is suitable for conjugation, a broad-host range and eliminates “all known problems associated with the heavily used E. coli S17-1/SM10 strains” (pg. 5, col.2, last para.). Strand et al. teach utilizing a TrfA in the TAmob plasmid (fig. 2).
Therefore, prior to the effective filing date of the instant invention it would have been prima facie obvious to one of ordinary skill in the art to modify the teachings of Ruotsalainen et al. and of Bonaterra et al. by substituting the pTA-mob plasmid taught by Strand et al. because the pTA-mob plasmid if more efficient and has a wide host range. Since, Strand et al’s. pTA-mob inherently comprises a TrfA, then it would be it is included in the vector construction.
One would have a reasonable expectation of success in doing so because each of Ruotsalainen et al., and Strand et al. teach the successful application of modifying bacteria to transfer DNA to kill recipient bacteria.
Therefore, the claimed invention is obvious over the prior art.
Subject matter is free from the art
In regard to claims 9, 11 and 20 are free from the art. The closest prior art is Strand et al., (PLoS ONE, Vol. 9(3): e90372, 2014, https://doi.org/10.1371/journal.pone.0090372 (Y) that fails to discloses mutations in the TrfA and the specific sequences for TrfA and pirA.
In regard to claim 13 is free from the art. The closest prior art is Hamilton et al., (Nat. Commun., Vol. 10, Article 4544, 2019, https://doi.org/10.1038/s41467-019-12448-3.(U)) that fails to teach on targeting non-coding regions.
Conclusion
No claims are allowed.
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/C.J.O./Examiner, Art Unit 1663
/JASON DEVEAU ROSEN/Primary Examiner, Art Unit 1662
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