DETAILED ACTION
Notice of Pre-AlA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. The amendment filed on June 29, 2026, has been received and entered.
Claim Disposition
3. Claims 4-17, 20-49, 51-72 and 74-75 have been cancelled. Claims 1-3, 18-19, 50, 73 and 76 are pending and are under examination.
Claim Objection
4. Claims 1-3, 18-19, 50, 73 and 76 are objected to because of the following informalities:
For clarity and precision of claim language it is suggested that claim 1 is amended to read, “……(a) a pathway…….[[and]] (b) a non-phosphotransferase system……. and (c) a modification…..….. selected from the group consisting of E. coli ptsI [[or]] and E. coli ptsI homologs; and wherein the non-natrual E. coli microbial organism has increased……..”. The dependent claims hereto are also included.
For clarity it is suggested that item 1(b) is amended to recite the discrete sequence notation for the nucleic acids (i.e., SEQ ID NO:). See also claims 2-3 with similar language.
For clarity it is suggested that claim 2(ii) is amended to recite proper Markush language which should be, for example, ‘A, B and C’; (note that the language has ‘and, or, and, or).
For clarity it is suggested that claim 76 is amended to read, “[[where]] wherein the…’.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
5. Claims 1-3, 18-19, 50, 73 and 76 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.
The claimed invention is directed to “a non-natural E. coli microbial organism which produces acetyl-CoA; or acetyl-CoA and oxalacetate, wherein the organism comprises: a PK pathway comprising phosphoketolase selected from the group recited in claim 1, a non-PTS for sugar uptake with modification and a modified PTS activity (see claim 1 in its entirety). However, the claimed invention does not set forth the specific modification for the increase in non-PTS or a modification that attenuates or eliminates PTS activity (see claims 1, 3, for example). The invention of claim 1 encompasses a modification that attenuates or eliminates a phosphotransferase activity wherein the modification comprises attenuation of the expression of or deletion of a nucleic acid selected from the group consisting of E.coli ptsI or homologs (which is not specific). The claim language does not set forth how attenuation is achieved and what specific homolog. Moreover, the invention indicates that the organism further comprise one or more modifications to the electron transport chain of the organism, or attenuation or deletion of an endogenous nucleic acid encoding a NADH dependent dehydrogenase selected from the group consisting of E. coli etc, which is not adequately described. This language does not inform the ordinary skilled worker what specific modifications; and what modifications produces the desired results. In addition, the claimed invention encompasses several exogenous genes that is not adequately described and homologs thereof, see for example, claims 1-3, which are not defined or adequately described. Further, the claimed invention is directed to a non-natural organism that is not provided (i.e., is it a bacteria, fungus, yeast (see claim 1 for example) in the independent claims and ‘non-natural’ can simply be a mutation or modification, however, not clearly defined. Several claims recite that the modification can be increase of non-PTS activity, however, there’s no indication of how much of an increase is desirable. The increase is also recited as being attributed to increased expression or activity of for example, a non-PTS permease, a facilitator protein etc., however, no specific mechanism or methodology. There is no one-to-one correspondence between any or all facilitator proteins, for instance and a measurable increase of non-PTS activity to demonstrate possession of the large genus encompassed in the claims. It is noted that claim 18 recites that the sugar uptake can be for instance 125% or 150% greater than the rate of sugar uptake in an organism that does not comprise the modification. But there is no specific modification identified with the aforementioned increase as being responsible and there is no base line to compare with for the increased amounts. The claimed invention is overly broad and not adequately described, with a large amount of variability/genus such as exogenous genes encoding PK pathway enzymes.
Thus, the claimed invention is not adequately described and devoid of any activity, and no structure-function correlation is made.
The specification fails to provide any additional representative species of the
claimed genus to show that applicant was in possession of the claimed genus.
A representative number of species means that the species which are
adequately described are representative of the entire genus. 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, disclosure of
drawings, or by disclosure of relevant identifying characteristics, for example, 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.
An applicant shows possession of the claimed invention by describing the claimed invention with all of its limitations using such descriptive means as words, structures, figures, diagrams, and formulas that fully set forth the claimed invention. See Lockwood v. American Airlines, Inc., 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir.1997). Thus, applicant has not demonstrated possession of the invention as claimed. Furthermore, the 'written description' requirement.., serves both to satisfy the inventor's obligation to disclose the technologic knowledge upon which the patent is based, and to demonstrate that the patentee was in possession of the invention that is claimed ....The descriptive text needed to meet these requirements varies with the nature and scope of the invention at issue, and with the scientific and technologic knowledge already in existence." Capon v. Eshhar, 418 F.3d 1349, 1357 (Fed. Cir. 2005). The purpose of the written description requirement "is to ensure that the scope of the right to exclude ... does not overreach the scope of the inventor's contribution to the field of art as described in the patent specification." Reiffin v. Microsoft Corp., 214 F.3d 1342, 1345-46 (Fed. Cir. 2000). The goal of the written description requirement is "to clearly convey the information that an applicant has invented the subject matter which is claimed." In re Barker, 559 F.2d 588, 592 n.4 (CCPA 1977) "A disclosure in an application, to be complete, must contain such description and details as to enable any person skilled in the art or science to which the invention pertains to make and use the invention as of its filing date." In re Glass, 492 F.2d 1228, 1232 (CCPA 1974).
Additionally, Vas-Cath Inc. v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Fed. Cir.1991), states that "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). The skilled artisan cannot envision the detailed chemical structure of the encompassed genus of cells and compounds etc., therefore, 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).
Accordingly, the claimed invention is determined as lacking adequate written description because applicant has not demonstrated possession of the entire genus encompassed in the claims, which is vast.
Response to Arguments
6. Applicant’s comments have been considered in full. Withdrawn objections/rejections will not be discussed herein as applicant’s comments are moot. Note that some objections remain as well as have been instituted for the reasons stated above and because not all issues raised were addressed. In addition, the rejection under 112 first paragraph remains and has been altered to reflect changes made to the claims. Applicant traverses the rejection stating that the claim 1 has been amended to recite specific phosphoketolase enzyme, modification to increase non-PTS activity (increased expression of one or more identified nucleic acids). This argument is not persuasive because the modification is not as specific as applicant is arguing. E. coli has more than one non-PTS system and the recitation of “increase non-TPS activity” is not specific, there’s no baseline or quantifiable amount. Further, the claim recites that the modification comprises increased expression of oner or more nucleic acids, and there is not defined way to increase the expression of the genes singly or in combination (if two or more of these genes are present then an inherent increase is possible, or did for a strong promoter or more copy numbers get introduced). Applicant also argues that a modification to attenuate or eliminate a PTS activity of specifically identified nucleic acid is provided, however, again the language is not very specific as asserted. A gene can be deleted and no additional explanation is needed, but how did applicant ‘attenuate the gene’. A specific outcome is claimed but specific parameters are not provided for an ordinary skilled worker to envision how the outcome was achieved. The claimed invention remains overly broad and not commensurate in scope with the disclosure. Applicant is arguing a specific scope not present in the claims because the language is not ‘specific’. The invention does not provide any structure for the gene that is in the non-natural microorganism that will encode the enzymes. Applicant further points out amendments made to other claims, which is also not persuasive as the invention as claimed requires not just the origin of the gene but the gene itself. The issue at hand is that the limitation of the specification cannot be read into the claims and a genetic modification is not descriptive with respect to what is actually altered to get the desired results. The claims are overly broad and do not define limitations that need to have concrete information. The claims recite the broad language of “modification” and then provides a resulting effect without the mechanism involved to achieve the desired results. Applicant provided excerpts from the specification which strengthens the need for this rejection because the language in the specification is also broad. Accordingly, the claimed invention is determined as lacking adequate written description because applicant has not demonstrated possession of the entire genus encompassed in the claims, which is vast. The examiner would welcome an opportunity to discuss the remaining issues.
Conclusion
7. No claims are presently allowable.
8. Applicant’s amendment necessitated the new/modified ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to HOPE A ROBINSON whose telephone number is (571)272-0957. The examiner can normally be reached 9-5pm, Monday to Friday.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert Mondesi can be reached on (408)918-7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/HOPE A ROBINSON/Primary Examiner, Art Unit 1652
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