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 .
Priority
This application was filed 10/11/2023.
Status of the Applications, Amendments and/or Claims
This action is written in response to applicant's correspondence submitted 02/19/2026. In the paper of 02/19/2026, Applicant amended claims 1-7.
Election/Restrictions
Applicant's election with traverse of group I (claims 1-5) in the reply filed on 02/19/2026 is acknowledged.
The traversal is on the ground(s) that the Office’s position that groups Inventions (I or III) and II are unrelated because the different inventions recite different processes is not accurate and that the claims are all related to a method of detection in an organic sample in a container by a CRISPR/Cas system.
This argument is not found persuasive since group I is drawn to method(s) for detection of a microorganism in an organic sample in a container by a CRISPR/Cas system for cutting a pre-defined part of the microorganism genome if the microorganism tested for is present. This method comprises an active step to be practiced by an ordinary skilled practitioner: i.e. a step of cutting a pre-defined part of a microorganism genome if the microorganism tested for is present in the test.
The method of group I suggests the group encompasses a couple of process steps that are not explicitly claimed: i.e. a step of ligating a cut part of the microorganism's genome and a nucleotide sequence coding for a reporter molecule with a partly complete promotor element/ start codon to form a complete promotor element or start codon and a step providing RNA polymerase and the complete promotor element or start codon to generate mRNA and/or to synthesize the reporter molecule.
The Office asserts that the methods of group I above, is distinct from the method of group II (claim 6) since group II recites only a single active process step for the detection of an unknown microorganism in an organic sample, i.e. a step of sequentially identifying the unknown microorganism by combining the unknown sequence from the microorganism with main categories within a phylogenetic tree, and thereafter test the unknown gene sequence against other sequences in the under category, which is repeated until the microorganism is finally identified.
The Office also asserts that the methods of group I above, is distinct from the method of group III (claim 7). First, the preamble of group III (claim 7) is directed to detection of a disease caused by a known gene mutation in an organic sample in a container by a CRISP/Cas-system, which has a different scope from the methods of group I, methods for detection of a microorganism in an organic sample in a container by a CRISPR/Cas-system. The methods of group III omit to make clear how confirming the presence of a microorganism in an organic sample is related to identifying a disease caused by a known gene mutation in an organic sample; or recite any additional process steps that relate to achieving the preamble’s goals.
The requirement is still deemed proper in view of the Office statements above and is therefore made FINAL.
Claims 5-6 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention(s), there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 02/19/2026.
Status of the claims
Claims 1-7 are pending. Claims 1-5 are currently under review.
Specification
The disclosure is objected to because of the following informalities: There is a lack of disclosure in the specification of reporter molecules causing a change of light intensity in a test, in a manner as presently recited by claim 4 or as written support for the subject matter of claim 4. Appropriate correction is required.
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 1-5 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.
Claim 1 recites the limitation of “cutting a pre-defined part of a microorganism genome if the microorganism tested for is present in the test, wherein a nucleotide sequence coding for a reporter molecule with a partly complete promotor element/ start codon is ligated with the cut part of the microorganism's genome thereby forming a complete promotor element or start codon that produces mRNA by RNA polymerase resulting in a chain of amino acids that can be detected and thereby verify the presence of the microorganism in the sample”.
Claim 1 lacks clarity and clarity of scope as only a conditional step of cutting a pre-defined part of a microorganism genome is actively recited.
Claim 1 fails to provide any functional role for CRISPR-Cas system, particularly failing to recite whether or not CRISPR-Cas participates in cutting the microorganism’s genome if present. Claim 1 is indefinite as the preamble directs the use of CRISPR-Cas system. However, the body of claim 1 lacks any active, positive steps delimiting how this use is actually practiced. Ex parte Erlich, 3 USPQ2d 1011 (Bd. Pat. App. & Inter. 1986).
Furthermore, it is unclear what process steps should be practiced in claim 1 or carried out by an ordinary skilled artisan so as to detect a microorganism of an organic sample, when a microorganism tested for is NOT present in the sample/test.
Claim 1 is further rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential steps, such omission amounting to a gap between the steps. See MPEP § 2172.01.
The omitted steps are:
combining CRISPR-Cas system and an organic sample comprising a microorganism genome and cutting a pre-defined part of the microorganism genome with the CRISPR-Cas system thereby generate a cut part of the microorganism genome;
ligating a nucleotide sequence encoding a reporter molecule and a truncated promotor element/ start codon with the cut part of the microorganism's genome, thereby forming a complete promotor element or start codon;
producing mRNA by providing RNA polymerase to the ligation product comprising complete promotor element or start codon and nucleotide sequence encoding a reporter molecule;
generating a chain of amino acids from the ligation product and detecting the reporter molecule, wherein detecting indicates the presence of the microorganism in the sample.
Claims 2-5 are rejected as they depend from claim 1.
Claim 1 is again rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite and lacking in clarity because the single active process step recited by claim 1 fails to provide a reasonable way to achieve the goal of the preamble of claim 1. Claim 1 recites a single step of cutting a pre-defined part of the microorganism genome and fails to make clear how the presence of the microorganism in the sample is to detected by the step of cutting. Claims 2-5 are also rejected as they depend from claim 1.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-5 are rejected under 35 U.S.C. 101 because the claims are not fully directed to patent eligible subject matter because of conditional nature of claim 1.
Claim 1 recites the limitation “cutting a pre-defined part of a microorganism genome IF the microorganism tested for is present in the test”.
Claims 1-5 are rejected under 35 U.S.C. 101 as these claims encompass a step of NOT cutting a pre-defined part of a microorganism genome, and doing nothing.
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 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wang et al. (December 2022, Mlife, 1(4), pp.412-427).
Regarding claim 1, Wang et al. teach genome editing for T. thermophilus HB27, a gram-positive bacterium/microorganism (abstract) utilizing genome-editing plasmids carrying an artificial self-targeting mini-CRISPR and a donor DNA responsible for the recombinant recovery (abstract and pg 414, left col, 1st para).
Wang et al. teach “additionally, we developed a reporter gene system for T. thermophilus based on a heat-stable β-galactosidase gene TTP0042, and constructed an engineered strain with a high production capacity of superoxide dismutases (SOD) by genome modification” (abstract and pg 414, left col, 1st para).
Regarding claim 1, Wang et al. teach cutting a pre-defined part of a microorganism genome (with endogenous CRISPR-Cas systems of type I-B and I-C and type III-A/B) and HDR repair events in T. thermophilus HB27 cells (see pg 417, Fig. 3).
Regarding claims 1 and 3-5, Wang et al. teach constructing of plasmid for genome editing in two steps: generating a self-targeting plasmid (pg 424, section entitled “Plasmid construction”) and a plasmid expressing β-glycosidase (pg 419, all text of “Construction of the reporter gene system for T. thermophilus HB27” and pg 424, section entitled “Plasmid construction”). Wang et al. then teach transformation of the pRKP31-TTP0042 plasmid into T. thermophilus HB27 cells (pg 419, all text of “Construction of the reporter gene system for T. thermophilus HB27” and pg 424, section entitled “Plasmid construction” and all text of pg 420).
Wang et al. teach transformation and protein expression of β-galactosidase reporter and X-gal screening and SOD expression (pg 419, all text of “Construction of the reporter gene system for T. thermophilus HB27” and pg 424, section entitled “Plasmid construction” and all text of pg 420 and teach SOD expression: pg 420, right col., section entitled “Increase in SOD production by integrating the SOD expressing cassette into the genome”).
Regarding claims 1 and 3-5, Wang et al. illustrates changes originating from reporter (pg 422, Figs. 8A-8D).
Accordingly, the instant claims 1-5 are anticipated by Wang et al.
Conclusion
No claims are currently allowed.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to OLAYINKA A OYEYEMI whose telephone number is (571)270-5956. The examiner can normally be reached Monday -Thursday: 9:00 am - 5:00 pm, EST.
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OLAYINKA A. OYEYEMI
Examiner
Art Unit 1681
/OLAYINKA A OYEYEMI/Examiner, Art Unit 1681
/GARY BENZION/Supervisory Patent Examiner, Art Unit 1681