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 41 and 52-70 are pending.
Claims 52-56 and 61-70 are withdrawn.
Claims 41 and 57-60 are under examination.
Election/Restrictions
Applicant’s election without traverse of the following invention
Invention
Group IV, claim 41, drawn to a method of identifying conditions for genetically modifying a prokaryotic species present in a heterogeneous population of prokaryotic cells, the method comprising: a) contacting the heterogeneous population of prokaryotic cells with a library of nucleic acids according to claim 37 under conditions that promote introduction of nucleic acid into a prokaryotic cell, wherein said contacting generates a modified heterogeneous population of prokaryotic cells comprising genetically modified prokaryotic cells comprising the transposon inserted into the genome; and b) identifying the species of genetically modified prokaryotic cells by sequencing the junction between the transposon and genomic DNA and/or by sequencing the nucleotide sequence barcode.
in the reply filed on 8th, December, 2025 is acknowledged.
It is noted that newly added claims 57-60 are also part of the elected group and are therefore under examination in this office action.
Newly submitted claims 52-56 and 62-70 directed to an invention that Lacks Unity with the elected invention for the following reasons:
Claims 52-56 and 61-70 are drawn to a method comprising introducing the prokaryotic cell a transposon system comprising: (i) a nucleotide sequence encoding polypeptides that form a CRISPR-associated transposase (CAST) complex; (ii) a nucleotide sequence encoding a guide RNA comprising a nucleotide sequence that hybridizes to a target nucleotide sequence in the target prokaryotic cell's genome; and (iii) a second transposon of interest flanked by recognition sites that are recognized by the CAST complex, wherein (i) and (ii) are present on the same nucleic acid construct. These claims are drawn to method steps of editing the genome of a target prokaryotic cell and accordingly are grouped with non-elected group II, as set forth in the Lack of Unity mailed on 10th, December, 2025.
Although claim 52 recites “The method of claim 41, further comprising: introducing into a target prokaryotic cell of said identified prokaryotic species susceptible to genetic modification, a transposon system comprising: (i) a nucleotide sequence encoding polypeptides that form a CRISPR-associated transposase (CAST) complex; (ii) a nucleotide sequence encoding a guide RNA comprising a nucleotide sequence that hybridizes to a target nucleotide sequence in the target prokaryotic cell's genome; and (iii) a second transposon of interest flanked by recognition sites that are recognized by the CAST complex, wherein (i) and (ii) are present on the same nucleic acid construct” which is claimed as an additional step and depending on claim 41, this is not a method “identifying, within a first heterogeneous population of prokaryotic cells, a prokaryotic species susceptible to genetic modification using a non-targeted transposon system” (preamble of claim 41), and is instead a method of editing the genome of a target prokaryotic cell. As such, it is a distinct method and has been grouped in non-elected Group II which is drawn to a method of editing the genome of a target prokaryotic cell with a transposon, as discussed above, that includes a CAST complex and comprises materially distinct method steps that do not align with the preamble of the elected group.
Accordingly, claims 52-56 and 61-70 withdrawn from consideration as being directed to a non-elected invention. See 37 CFR 1.142(b) and MPEP § 821.03.
Objections to Drawings
The drawings are objected to because they do not conform to sequence rules, requiring the use of “SEQ ID NO:” (37 CFR 1.821-1.825)(see also MPEP 2422.01).
The amino acid sequences in Figures 31A and 31C are not labeled with a corresponding sequence identifier.
Where the description or claims of a patent application discuss a sequence that is set forth in the “Sequence Listing” in accordance with paragraph (c) of this section, reference must be made to the sequence by use of the sequence identifier, preceded by “SEQ ID NO:” in the text of the description or claims, even if the sequence is also embedded in the text of the description or claims of the patent application. 37 CFR 1.821 (d).
The applicant is reminded that claims and specification must be amended in order to comply with regulations cited above. All references to sequences in the drawings, claims and specification should be referred to as “SEQ ID NO:1”, for example. To avoid all doubts of the examiner and to ensure correct interpretation of the claims and specification, the identification of sequences with proper sequence identifiers is required.
Objections to Specification
Browser Executable Code
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (http://n2t.net/addgene:127921 para. [00222], http://n2t.net/addgene:127921 para. [00222], https://doi.org/10.1101/2020.04.29.067207 para. [00232], https:(//)github.com/najoshi/sickle para. [00233], https: (//)github.com/christophertbrown/bioscripts para. [00233], https: (//)ggkbase.berkeley.edu para. [00233], https: (//)app.gitbook.com/@sdiamond/s/etsuite/etdb/etdb par. [00234], and https:// at github(dot)com/SDmetagenomics/ETsuite and Methods para. [00255]).
Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
This objection would be overcome if the embedded hyperlink and/or other form of browser-executable code is removed, or the reference to the website is amended to be limited to the top-level domain name.
Claim Rejections - 35 USC § 112(b)
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.
Claim 60 is 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.
Claim 60 recites “the first heterogeneous population of prokaryotic cells is present in: a mammal's gastrointestinal tract, a human's microbiome, a non-human animal's microbiome, soil, a hot spring, an ocean, a marshland, a swamp, wastewater, agricultural runoff, a fermentation that relies on a mixed community of cells to produce beverages or food, a rhizosphere, a plant microbiome, an industrial process that relies on a community of microorganisms, an industrial wastewater treatment process that relies on a community of microorganisms, or a bioreactor used for bioremediation of wastes.” It is unclear whether the recited limitation “is present in” refers to an active method step of the location of the species during the method, or whether this describes the natural location of the prokaryotic bacteria which is a characteristic of the bacteria. Further, it is unclear how prokaryotic cells could be contacted with a library of nucleic acids in the recited locations.
Claim Interpretation
Due to the 112b issues identified above, for the sake of compact prosecution, the claims identified with 112 issues above are being examined against the prior art and double-patenting as follows:
Claim 60 is interpreted as the first heterogeneous population of prokaryotic cells is sampled from (or is otherwise normally present in) the recited locations. This is in light of the instant specification which states that “target prokaryotic cells include prokaryotic cells found in a natural environment such as the gastrointestinal tract of a mammal (e.g., a human); the microbiome of a human; the microbiome of a non-human animal soil; hot springs; oceans; marshland; swamps; etc. Target prokaryotic cells include prokaryotic cells found in wastewater, agricultural runoff, and the like.
Target prokaryotic cells include prokaryotic cells involved in food processing (e.g., fermentations to produce beverages or food that rely on a mixed community of cells such as with
kimchi, soy sauce, or kombucha)” (para. [0099]).
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.
Claims 41 and 57-58 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wetmore et al. (mBio. 2015 May 12;6(3):e00306-15.; henceforth “Wetmore”).
Regarding claim 41, Wetmore discloses a method comprising:
a) contacting the first population of prokaryotic cells with a library of nucleic acids, wherein each member of the library comprises:
(i) a nucleotide sequence that is operably linked to a promoter and encodes a non-targeted transposase (transposon vectors);
(ii) a nucleotide sequence encoding a first transposon flanked by recognition sites that are cleaved by the non-targeted transposase (IRs);
and (iii) a unique (primers used in included unique 8-bp indexes that were sequenced “in line” with the random DNA bar code which means the barcodes were also unique; pg. 12 col. 1 2nd para.; see also “No. of strains with unique bar codes” Table 1 and “the strains have unique bar codes” pg. col. 1 2nd para.) nucleotide sequence barcode that identifies the first transposon and/or the promoter
thereby generating genetically modified prokaryotic cells comprising the first transposon inserted into the genome; and
b) sequencing the junction between the first transposon and genomic DNA (TnSeq) and/or by sequencing the nucleotide sequence barcode (BarSeq) (“both the DNA bar code and the transposon insertion site are identified in a single 150-nucleotide Illumina sequencing read” Figure 1).
Regarding claim 41, concerning the recited limitation that the population of prokaryotic cells is heterogenous, because the cell strains exhibited different phenotypes (see Table 1 “No. with significant phenotype” ; Table 1), the strains have phenotypic heterogeneity and therefore are encompassed by the broadest reasonable interpretation of “heterogenous.”
Regarding step b) or claim 41, although Wetmore is silent to a result of “identifying the species of the genetically modified prokaryotic cells” and “identifying said prokaryotic species susceptible to genetic modification” as recited in the thereby clause, the active method step of b) as claimed is “sequencing the junction between the first transposon and genomic DNA and/or by sequencing the nucleotide sequence barcode” which is disclosed by Wetmore as discussed above. Therefore, because Wetmore discloses the active method step of step b), the claimed results of “identifying the species of the genetically modified prokaryotic cells” and “identifying said prokaryotic species susceptible to genetic modification” would inherently follow the recitation of the disclosed steps and therefore the disclosure of Wetmore anticipates the limitations of step b) as claimed.
Regarding the preamble of claim 41, the preamble merely states, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations (see MPEP 2111.02) See also Rowe v. Dror, 112 F.3d 473, 478, 42 USPQ2d 1550, 1553 (Fed. Cir. 1997) As discussed above, Wetmore discloses all the active method steps of the instantly claimed method and therefore the method of Wetmore is capable of meeting the intended use identifying, within a first heterogeneous population of prokaryotic cells, a prokaryotic species susceptible to genetic modification using a non-targeted transposon system.
Regarding claim 57, further to the discussion of claim 41 above, Wetmore discloses the non-targeted transposon system is a Tn5 system (abstract; pg. 2 col. 2 2nd para.; Figure 1; Table 1; pg. 9 col. 1 3rd and 4th para.; pg. 10 col. 1; pg. 10 col. 2 2nd para.) or Mariner system (abstract; pg. 2 col. 1 1st para., col. 2 2nd para; Figure 1; Table 1; pg. 9 col. 1 2nd para., col. 2 2nd para.; pg. 10 col. 2 2nd para.).
Regarding claim 58, further to the discussion of claim 41 above, Wetmore discloses sequencing the junction (TnSeq) comprises:
fragmenting DNA obtained from the genetically modified prokaryotic cells (shearing genomic DNA);
ligating adaptor DNA fragments to the fragmented DNA (ligating adapters) (“In TnSeq, genomic DNA is sheared, end repaired, and ligated with Illumina Y adapters”; Figure 1 legend); and
amplifying the junction between the first transposon and the genomic DNA by polymerase chain reaction (PCR) (PCR that amplifies the transposon junction using primers that are complementary to the adapter and to the transposon), using a forward PCR primer that hybridizes to a nucleotide sequence in the first transposon and a reverse PCR primer that hybridizes to a nucleotide sequence in the adaptor DNA (“one primer specific to the Y adapter and a second primer specific to the transposon” ; Figure 1 legend) (pg. 2 col. 2 2nd para.; Figure 1B; see also Table S2).
Accordingly, Wetmore anticipates instant claims.
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.
Claims 59-60 are rejected under 35 U.S.C. 103 as being unpatentable over Wetmore et al. (mBio. 2015 May 12;6(3):e00306-15.; henceforth “Wetmore”) in view of Rey et al. (Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13582-7. Epub 2013 Jul 29.; henceforth “Rey”).
The teachings of Wetmore above are hereby incorporated in their entirety.
Regarding claim 59, although Wetmore teaches the method can be applied to diverse bacteria and is a powerful tool to annotate uncharacterized genes using phenotype data (abstract), and Wetmore teaches pooled mutant fitness assays can also be used to assay growth in cocultures, growth in mice, motility, or survival, or to identify strains with altered morphology after separation with a cell sorter (pg.9 col. 1 4th para.) Wetmore is silent to performing the method on a first heterogenous population of cells that comprises at least 5 different species of prokaryotic cells.
Nevertheless, regarding claim 59, Wetmore cites Rey (pg.9 col. 1 4th para.; citation 29). Rey teaches a method comprising performing transposon mutagenesis on samples from mice colonized with 9 bacterial species (pg. 13583 col. 1; see also “Nine-Member Artificial Community” SI results pg. 1 col. 1) to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common Sulfate-reducing bacteria in a surveyed cohort of healthy US adults (abstract).
Therefore, regarding claim 59, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention or practice the method of Wetmore, and combine the known prior art element of the target population of 9 bacterial species of Rey to obtain the predictable result of a method to assay fitness. One of ordinary skill would have been motivated to do so as taught by Rey to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common Sulfate-reducing bacteria in a surveyed cohort of healthy US adults (abstract). Regarding the reasonable expectation of success, Wetmore evidences performing the transposon sequencing method on populations of prokaryotic bacteria (abstract; Figure 1; Table S1).
Regarding claim 60, further to the discussion of claim 41 above, the target bacteria suggested by Rey above (see claim 59 rejection above), are sampled from a mammal’s (mouse) gastrointestinal tract and are normally present in a humans gastrointestinal tract (pg. 13583 col. 1; see also “Nine-Member Artificial Community” SI results pg. 1 col. 1).
Hence, the claimed invention as a whole was prima facie obvious.
Conclusion
No claim is allowable.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIANA N EBBINGHAUS whose telephone number is (703)756-4548. The examiner can normally be reached M-F 9:30 AM to 5:30 PM ET.
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/BRIANA N EBBINGHAUS/Examiner, Art Unit 1632 /VALARIE E BERTOGLIO/Primary Examiner, Art Unit 1632