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 .
Election/Restrictions
Applicant’s election without traverse of Invention/Group I in the reply filed on 2 April 2026 is acknowledged.
Claims 31-36 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 2 April 2026.
Applicant’s election without traverse of Species SEQ ID NOs: 2 and 16 in the reply filed on 2 April 2026 is acknowledged.
Claims 30 and 36 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 2 April 2026.
Claim Status
Claims 17-36 are pending.
Claims 17 and 31 are currently amended.
Claims 30-36 are withdrawn from consideration.
Claims 17-29 are examined on the merits.
Claim Rejections - 35 USC § 112
Indefiniteness
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.
Claims 17-29 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 pre-AIA the applicant regards as the invention.
Items a) and b) of claim 17 recite, “obtaining the gDNA sequence of the translation initiation sequence (TIS) of a gene of interest encoding the protein or interest of the species,” and “b) comparing the gDNA sequence of the TIS of said gene with relative frequency of each nucleotide in one or more positions of the TIS in said species or highly similar species.”
These steps are both largely mental steps so it is unclear how they are intended to limit the claims. For example, if a person of ordinary skill in the art is working in a species that has a completely sequenced genome and thus know that the TIS for every gene is available in the database, is that enough to meet the limitation of the TIS being “obtained?” Or does the sequence of the TIS need to be saved to a computer? What if the sequence is accessed in a web browser, is that sufficient for it to be considered, “obtained?” If the browser window is closed, is the TIS sequence no longer “obtained?”
The idea of “comparing” sequences has the same issues. Unless you are able to read minds, it is impossible to determine whether someone has “compared” two sequences. Thus, it is unclear how this step could actually limit the claim. As such, the metes and bounds of the claim cannot be determined.
Additionally, item b) reciting, “highly similar species” without providing guidance in the specification as to what can and cannot be considered “highly similar.” As such, the metes and bounds of the claim cannot be determined.
Claims 18-29 are also rejected for depending from an indefinite claim and failing to recite additional limitations that would render the claims definite.
Item b) of claim 22 recites, “dividing said pool into one or more sub-pools…” How is possible to divide something and end up with only a single sub-pool? The step of “dividing” requires that at least two sub-pools are created. Given this confusing use of the word, “dividing,” the metes and bounds of the claims cannot be determined.
Claim 29 recites, “wherein the TIS of HvSUT2 gene in said variant comprises or consists of SEQ ID NO:2.” It is unclear how the TIS can consist of the 15 bp sequence set forth in SEQ ID NO:2. The claim requires that the TIS be endogenous, so the sequence will necessary be in the context of a chromosome. Moreover, claim 24 indicates that substitutions can be made in the TIS from positions -10 to +13. This suggests that the specification contemplates that the TIS is 23 bp in length. These two facts together, make it unclear how the TIS can consist of only the 15bp set forth in SEQ ID NO:2. As such, the metes and bounds of the claim cannot be determined.
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) 17-21, 23-25, and 27-28 is/are rejected under 35 U.S.C. 102(a)(1) as anticipated by Xu et al 2021 (Microbial Cell Factories 20:148, p.1-11) as evidenced by Hamilton et al 1987 (Nucleic Acids Research 15:8, p. 3581-3593).
Xu et al disclose altering the endogenous yeast HMG1 translation initiation sequence (Kozak). This was achieved by using a programmable Cas9 nuclease to make a target DSB in the region 5’ of the HMG1 gene to facilitate homologous recombination between the provided correcting template comprising the modified yeast HMG1 translation initiation sequence with the native chromosome. Four different variant translation initiation sequences (Kozak) were introduced into the HMG1 site (K0/540/536/528 whose sequences can be seen in Figure 3B, positions -9 to -1). Increased presence of the protein was measured presence of squalene which is the downstream product of the HMG-CoA reductase in yeast (thus measuring squalene is a measurement of in vivo HMG-CoA reductase activity (Figure 4). In the Background, Xu et al state the consensus Kozak sequence from yeast as was determined Hamilton et al in 1987. The changes in variants K0/540/536/528 comprise alterations of relative frequency at positions both increasing and decreasing from the relative frequency greater than 2.5% as determined by Hamilton et al. Accordingly, claims 17-21, 23-25, and 27-28 is/are rejected under 35 U.S.C. 102(a)(1) as anticipated by Xu et al as evidenced by Hamilton et al.
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.
Claim(s) 26 is/are rejected under 35 U.S.C. 103 as being unpatentable over Xu et al 2021 (Microbial Cell Factories 20:148, p.1-11) as evidenced by Hamilton et al 1987 (Nucleic Acids Research 15:8, p. 3581-3593).
Claim 26 is drawn to the method of claim 25, wherein the consensus matrix is obtained by analyzing TISs of more than 100 genes of the organism of interest.
Xu et al teach all the limitations of claim 25. Hamilton et al stated that their consensus matrix was obtained from analysis of 96 genes.
Xu et al do not teach wherein the consensus matrix is obtained by analyzing TISs of more than 100 genes of the organism of interest.
At the time of filing, it would have been prima facie obvious to generate a consensus matrix from yeast using a larger number of genes that 100 genes. When Hamilton et al published their work, the amount of sequence information from any organism was quite limited. By 1996, the entire yeast genome was known. Given the computing power and sequence information available in yeast, it would have been prima facie obvious for a person of ordinary skill in the art to expand upon the work of Hamilton et al and create a yeast TIS using all the TISs in the genome. A comprehensive TIS would have allowed a person of ordinary skill to better understand the frequencies of TISs such that alterations could be made from a more informed perspective. As such, claim 26 is rejected as being obvious over Xu et al as evidenced by Hamilton et al.
Claim(s) 22 is/are rejected under 35 U.S.C. 103 as being unpatentable over Xu et al 2021 (Microbial Cell Factories 20:148, p.1-11) as evidenced by Hamilton et al 1987 (Nucleic Acids Research 15:8, p. 3581-3593) and further in view of Lewis et al 2010 (Phytochemistry 71: p. 1988-1998).
Claim 22 is drawn to the method of claim 17 wherein variants are identified via a screening process comprising the steps set forth in the claim that requires creating pools and sub-pools of candidate organisms and having fractions of the candidate organisms available for potential multiplication of organism of each identified genotype. This initially appears complex but is seen as intuitive after briefly considering the steps. It essentially says to after you generate a pool of random organism to screen for having a mutation that you are looking for, keep enough of the organism alive that you can go back to once you have identified which organism or lineage of organism has the sought after mutation.
Xu et al teach all the limitations of claim 17.
Xu et al do not teach the screening process for variants comprising the steps set forth in the claim that requires creating pools and sub-pools of candidate organisms and having fractions of the candidate organisms available for potential multiplication of organism of each identified genotype.
Lewis et al teach such a method when they were attempting to isolate mutant alleles of tobacco genes of interest (p. 1990-1991). They first mutagenized a large population of tobacco seeds (M0 generation) and grew the mutagenized seeds to maturity to produce M1 generation of seed. A subset of M1 seed was grown and DNA was isolate from these plants, and the loci of interest were sequenced to identify individuals having SNPs in regions of interest. Lewis et al were then able to go back to other M1 seeds from the same M0 parent, such that they would be able to access plants having the SNPs for additional research and/or breeding steps.
At the time of filing, it would have been prima facie obvious to screen a population of candidate organism to identify individuals having alleles of interest using a scheme that allows to return to a pool of seeds, cells, or living tissue such more living individuals having the identified allele of interest can be generated. Such methos have been known and practiced in the art. One such example is the one taught by Lewis. Accordingly, claim 22 is rejected as being obvious over Xu et al as evidenced by Hamilton et al and further in view of Lewis et al 2010.
Comment on State of the Prior Art
The idea of changing a translation initiation sequence to alter the level of a protein within a cell has been understood for nearly thirty years. Kozak’s paper in Cell demonstrated that point mutations with the region surrounding the start ATG codon can greatly affect the amount of protein produced by a eukaryotic gene (Kozak 1986 (Cell 44: p. 283-292)). This work differs from the instant case being that the experiments were all done using transfected DNA constructs and not endogenous. In addition to the cited prior art Xu et al, Ambrosini et al 2021 (“Reprogramming translation for gene therapy,” Progress in Molecular Biology and Translational Science 182: p. 439-476) review work done targeting the native TIS (Kozak) sequence on several different genes to change protein expression levels (both increase and decrease). Several of the studies cited by them are closely related to the instantly claimed subject matter.
The question that remains is the notion of determining which mutations to make by determining nucleobase frequencies of each site in the TIS with an organism or group of related organisms. Agarwal et al 2009 (Plant Cell Reports 28: p. 1791-1798) did just that. In efforts to optimize protein expression of a recombinant human proteinase inhibitor in tomato, they analyzed the Kozak sequence of highly expressed dicot genes to create a consensus matrix to help them determine which point mutations in the Kozak sequence would be most likely to increase the level recombinant protein produced (Table 1). Additionally, several large-scale bioinformatic studies have investigated variability of TISs across species (Hernandez et al 2019 (Trends in Biochemical Sciences 44:12, p. 1009-1021) and Gupta et al 2016 (Journal of Theoretical Biology 404: p. 303-311)).
This art has cited here in hopes that Applicant will consider it when making claim amendments in hopes moving prosecution forward.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MATTHEW R KEOGH whose telephone number is (571)272-2960. The examiner can normally be reached M-Th 7-4:30, half day on Fridays.
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/MATTHEW R KEOGH/Primary Examiner, Art Unit 1663
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