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 .
DETAILED ACTION
This Office Action is a response to Applicant’s Election filed August 4, 2026.
Claims 1-13, 15 and 17-21 are pending in the present application.
Election/Restrictions
Applicant’s election without traverse of Group IV (claims 17-21) in the reply filed on August 4, 2026 is acknowledged. Claims 1-13 and 15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 August 4, 2026.
The requirement is still deemed proper and is therefore made FINAL.
Accordingly, claims 17-21 have been examined on the merits as detailed below:
Information Disclosure Statement
Applicant’s information disclosure statement (IDS) filed November 16, 2023 is acknowledged. The submission is in compliance with the provisions of 37 CFR §1.97. Accordingly, the Examiner has considered the information disclosure statement, and a signed copy is enclosed herewith.
The listing of references at pages 39 and 40 in the Specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Drawings
It is noted that there are no Drawings associated with the present application.
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.
Claim 18 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 pre-AIA the applicant regards as the invention.
Claim 18 is indefinite because it is unclear whether parts following the term, “optionally” are actually a part of the claims. The term, “optionally” is ambiguous and confusing since the alternatives covered by the claims are not clear. See MPEP 2173.05(h) for further explanation.
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 17-21 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. This is a written description rejection.
The following quotation from section 2163 of the Manual of Patent Examination Procedure is a brief discussion of what is required in a specification to satisfy the 35 U.S.C. 112 written description requirement for a generic claim covering several distinct inventions:
The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice..., reduction to drawings..., or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus... See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
A "representative number of species" means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
Thus, when a claim covers a genus of inventions, the disclosure must provide written support for the entire scope of the genus. Support for a genus is generally found where the Applicant has provided a number of examples sufficient so that one in the art would recognize from the specification the scope of what is being claimed and that applicant was in possession of the claimed genus.
The claims are drawn to a method for producing an increased amount of a protein of interest (POI) comprising: (a) obtaining or constructing a parental Bacillus cell producing a POI and modifying the cell by introducing therein a polynucleotide encoding a phosphatidylserine synthase (PssA) protein comprising at least 85% sequence identity to SEQ ID NO: 17, and (b) cultivating the modified cell under suitable conditions for the production of the POI, wherein the modified cell produces an increased amount of the POI relative to the parental cell when cultivated under the same conditions. The present Specification teaches SEQ ID NO: 17 is the amino acid sequence of the B. licheniformis PssA protein encoded by SEQ ID NO: 16. See page 5. The present Specification also discloses at Example 1:
A PssA expression cassette comprising SEQ ID NO: 12 or SEQ ID NO: 27 was then integrated at the catH locus (SEQ ID NO: 13) of the amylase 1 production strain BF333. More particularly, the PssA expression cassettes contain the native B. licheniformis catH expression cassette (SEQ ID NO: 14) operably linked to the B. subtilis spoVG transcription terminator (SEQ ID NO: 15) operably linked to a promoter operably linked to the modified B. subtilis aprE 5′ UTR (SEQ ID NO: 6) operably linked to the B. licheniformis PssA ORF (SEQ ID NO: 16) operably linked to the B. licheniformis amyL transcriptional terminator (SEQ ID NO: 8). In the instant example, B. licheniformis tuf (SEQ ID NO: 18) and citZ (SEQ ID NO: 19) promoters were used to drive PssA expression (i.e., expression cassettes SEQ ID NO: 12 and SEQ ID NO: 27, respectively), and resulted in amylase 1 production strains named “ZM1021” and “ZM1022”, respectively.
The results shown in TABLE 1 demonstrate an improvement of amylase production in the strains comprising a second (2nd) copy of the native PssA gene (e.g. SEQ ID NO: 16) controlled by a heterologous promoter (e.g., either tuf or citZ promoter).
There is insufficient written description of the polynucleotide encoding a PssA protein comprising at least 85% sequence identity to SEQ ID NO: 17 encompassed by the claims. The present Specification discloses a sequence comprising SEQ ID NO: 17, but does not describe sequences with any percent identity to SEQ ID NO: 17 that function as claimed to encode a PssA protein. In other words, there is no teaching in the Specification regarding which 15% of the sequence structure can be varied and still produce the functional protein as recited. NOTE: The same rationale holds true for those claims reciting, “wherein the open reading frame (ORF) sequence encoding the PssA protein comprises at least 85% sequence identity to the nucleic acid sequence of SEQ ID NO: 16”.
Written description requirement for claims that recite a polynucleotide encoding a PssA protein comprising at least 85% sequence identity to SEQ ID NO: 17 is not met because the Specification does not provide any description of any variants or what sequences could be modified (added, deleted or mutated) that retain function. Accordingly, the claims encompass using a genus of polynucleotide sequence which are not adequately described. Therefore, the claims are rejected because there is insufficient description of the genus of polynucleotides encompassed by the claims.
Vas-Cath Inc. v. Mahurkar, 19USPQ2d 1111, clearly states “applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the ‘written description’ inquiry, whatever is now claimed.” (See page 1117.) The specification does not “clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed.” (See Vas-Cath at page 1116). It is noted that conception is not achieved until reduction to practice has occurred regardless of the complexity or simplicity of the method of isolation. Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method of isolating it. The compound itself is required. See Fiers v. Revel, 25 USPQ2d 1601 at 1606 (CAFC 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016.
To satisfy the written description requirement an applicant must describe the invention is such a way as to convey to one skilled in the art that applicant had the invention in his possession when the application was filed. Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010) (en banc). In cases such as the instant application where a genus is claimed, the specification must contain “either a representative number of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can ‘visualize or recognize’ the members of the genus.” Id. at 1350. However, written description requirement for claims that recite a polynucleotide encoding a PssA protein comprising at least 85% sequence identity to SEQ ID NO: 17 that function to encode a PssA protein is not met.
The entire genus of methods of using a polynucleotide encoding a PssA protein comprising at least 85% sequence identity to SEQ ID NO: 17 does not exist in the instant application. That is, adequate written description support does not exist to practice the full scope of the invention claimed. The specification nor the art discloses neither a representative number of species polynucleotides nor any structure/function correlation that would enable one of skill to immediately envision the genus of polynucleotide sequences required to practice the full scope of the invention.
As stated above, the MPEP states that written description for a genus can be achieved by a representative number of species within a broad generic claim. Given the breadth of the claims, the Specification lacks sufficient variety of species to reflect the variance in the genus.
In conclusion, the Specification and the prior art as filed does not provide sufficient descriptive support for the myriad of polynucleotide sequences embraced by the claims. For the reasons discussed above, the 35 USC § 112 rejection for written description is applicable.
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 set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) 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 17-21 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2008/066931 A2 (NOVOZYMES INC (5 June 2008) (submitted and made of record on the IDS filed November 16, 2023).
The claims are drawn to a method for producing an increased amount of a protein of interest (POI) comprising: (a) obtaining or constructing a parental Bacillus cell producing a POI and modifying the cell by introducing therein a polynucleotide encoding a phosphatidylserine synthase (PssA) protein comprising at least 85% sequence identity to SEQ ID NO: 17, and (b) cultivating the modified cell under suitable conditions for the production of the POI, wherein the modified cell produces an increased amount of the POI relative to the parental cell when cultivated under the same conditions.
NOVOZYMES is relevant and relied upon in its entirety. NOVOZYMES disclose:
The present invention also relates to recombinant expression vectors comprising an isolated polynucleotide of the present invention, a promoter, and transcriptional and translational stop signals. The various nucleic acid and control sequences described above may be joined together to produce a recombinant expression vector that may include one or more (several) convenient restriction sites to allow for insertion or substitution of the nucleotide sequence encoding the polypeptide at such sites. Alternatively, a polynucleotide of the present invention may be expressed by inserting the nucleotide sequence or a nucleic acid construct comprising the sequence into an appropriate vector for expression. In creating the expression vector, the coding sequence is located in the vector so that the coding sequence is operably linked with the appropriate control sequences for expression
NOTE: NOVOZYMES teaches that the term nucleic acid construct is synonymous with the term "expression cassette".
NOVOZYMES particularly teaches the sequencing of the Bacillus licheniformis genome and the identification of a polynucleotide encoding PssA via shotgun sequencing (SEQ ID NO: 3820, Table 1, page 220). SEQ ID NO: 16 from the present application has 100% identity (100% similarity) over the whole sequence to SEQ ID NO: 3820 from NOVOZYMES. Also, SEQ ID NO: 17 of the instant invention has 100% identity over the whole sequence to SEQ ID NO: 8695 from NOVOZYMES.
NOTE: The term 'protein of interest' as instantly claimed does not allow a distinction to be made between the Bacillus cell producing a protein of interest of NOVOZYMES and the invention, as any protein produced by the bacteria could be this protein. For example, NOVOZYMES are explicit in disclosing the expression of a plurality of genes from a Bacillus cell and more than one copy of a polynucleotide of the present invention may be inserted into the host cell to increase production of the polynucleotide product. Also, NOVOZYMES teach mutant cell producing less of the biologically active substance than the parent cell when cultivated under the same conditions.
NOVOZYMES does not necessarily teach the method of their invention leads to increased amount of a POI relative to the parental cell when cultivated under the same conditions, however, NOVOZYMES teaches the same method steps (a) and (b) as claimed. Any underlying mechanism of action would naturally flow and be inherent to carrying out the method steps of the prior art disclosure. See MPEP 2112 as it relates to inherency.
Furthermore, the instant specification serves as evidence of record establishing this inherency. Failure of those skilled in the art to contemporaneously recognize an inherent property (i.e. a biological mechanism of action) of a prior art reference does not preclude a finding of anticipation. Atlas Powder Co. v. IRECO, Inc., 190 F.3d 1342, 1349, 51 USPQ2d 1943, 1948 (Fed. Cir. 1999). See also Ex parte Novitski, 26 USPQ2d 1389 (Bd. Pat. App. & Inter. 1993).
Note that the Office does not have the facilities and resources to provide the factual evidence needed in order to determine that the method taught, suggested and motivated by NOVOZYMES would produce an increased amount of a protein of interest in a cell as presently claimed. In the absence of evidence to the contrary, the burden is upon the Applicant to prove that the presently claimed method is any different from the method disclosed by the prior art such that method of the prior art cannot have the intended use/functionality, thereby establishing patentable differences. See In re Best 562F.2d 1252, 195 USPQ 430 (CCPA 1977) and Ex parte Gray 10 USPQ2d 1922(PTO Bd. Pat. App. & Int. 1989).
The Examiner has provided sound basis in fact and technical reasoning that reasonably supports the determination that the allegedly inherent characteristic necessarily flows from what has been specifically disclosed within the prior art and has shifted the burden to Applicant to provide evidence to the contrary.
Before the effective filing date of the claimed invention, methods for producing encoded substances by cultivating a recombinant host cell such as a wild-type Bacillus strain and recovering the product were known in the prior art.
Methods for producing a biologically active substance comprising (a) cultivating a host cell under conditions conducive for production of the biologically active substance, and (b) recovering the biologically active substance are known and described in the art of NOVOZYMES. The “biologically active substance” is defined broadly to include polypeptides such as enzymes.
A person of ordinary skill in the art would have expected reasonable success to devise the methods of the claimed invention using the teachings and motivation of NOVOZYMES which teaches promoters, vectors, Bacillus and other host cells, transformation techniques and protein recovery methods.
Therefore, the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention.
Conclusion
No claims are allowable at this time.
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Terra C. Gibbs whose telephone number is 571-272-0758. The Examiner can normally be reached from 8 am - 5 pm M-F.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner's supervisor, Ram Shukla can be reached on 571-272-0735. 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.
Patent applicants with problems or questions regarding electronic images that can be viewed in the Patent Application Information Retrieval system (PAIR) can now contact the USPTO's Patent Electronic Business Center (Patent EBC) for assistance. Representatives are available to answer your questions daily from 6 am to midnight (EST). The toll free number is (866) 217-9197. When calling please have your application serial or patent number, the type of document you are having an image problem with, the number of pages and the specific nature of the problem. The Patent Electronic Business Center will notify applicants of the resolution of the problem within 5-7 business days. Applicants can also check PAIR to confirm that the problem has been corrected. The USPTO's Patent Electronic Business Center is a complete service center supporting all patent business on the Internet. The USPTO's PAIR system provides Internet-based access to patent application status and history information. It also enables applicants to view the scanned images of their own application file folder(s) as well as general patent information available to the public.
For all other customer support, please call the USPTO Call Center (UCC) at 800-786-9199.
/TERRA C GIBBS/Primary Examiner, Art Unit 1635
Prosecution Insights