DETAILED ACTION
Election/Restrictions
Applicant's election with traverse of Group I, claims 1-8 and 10, in the reply filed on 12/11/25 is acknowledged. The traversal is on the ground(s) that claims have been amended to depend on claim 1 and that the references cited, Reed et al and Feinberg et al, do not have a motivation to combine. Applicants’ arguments are presented on pages 7-11 of the response. These arguments have been fully and carefully considered but are not found persuasive. With respect to the argument that Reed and Feinberg provide no teaching, suggestion, or motivation to combine the references, the examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In this case, the prior art has taught that the PHA polymer is poly(3-hydroxybutyrate) (PHB) which is rarely digestible and offers little to no nutritional value. The PHB component also reduces the protein content of the organism. In addition, non-nutritive PHB storage compound in the cytoplasm takes up physical space, leaving less space for nutritive compounds. Further, in some instances, the PHB components had a detrimental impact on biological functions, such as digestive system processes. The combination of Reed and Feinberg, along with Pearlman below, teach PHB production in the organism is attenuated or eliminated by modifying one or more of the phaCAB operon enzymes which enable the strain to produce PHB. The chemoautotrophic bacteria in the prior art references are considered “variants of VTT-E-193585.
With respect to the withdrawn process claims and their dependence on claim 1, the examiner has required restriction between product or apparatus claims and process claims. Where applicant elects claims directed to the product/apparatus, and all product/apparatus claims are subsequently found allowable, withdrawn process claims that include all the limitations of the allowable product/apparatus claims should be considered for rejoinder. All claims directed to a nonelected process invention must include all the limitations of an allowable product/apparatus claim for that process invention to be rejoined.
In the event of rejoinder, the requirement for restriction between the product/apparatus claims and the rejoined process claims will be withdrawn, and the rejoined process claims will be fully examined for patentability in accordance with 37 CFR 1.104. Thus, to be allowable, the rejoined claims must meet all criteria for patentability including the requirements of 35 U.S.C. 101, 102, 103 and 112. Until all claims to the elected product/apparatus are found allowable, an otherwise proper restriction requirement between product/apparatus claims and process claims may be maintained. Withdrawn process claims that are not commensurate in scope with an allowable product/apparatus claim will not be rejoined. See MPEP § 821.04. Additionally, in order for rejoinder to occur, applicant is advised that the process claims should be amended during prosecution to require the limitations of the product/apparatus claims. Failure to do so may result in no rejoinder. Further, note that the prohibition against double patenting rejections of 35 U.S.C. 121 does not apply where the restriction requirement is withdrawn by the examiner before the patent issues. See MPEP § 804.01.
The requirement is still deemed proper and is therefore made FINAL.
Claims 1-8 and 10 are currently under examination.
Claims 11-33 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention.
Claim Rejections - 35 USC § 112-Deposit Information
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 1-8 and 10 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
The specification lacks complete deposit information for the deposit of bacterial strains VTT-E-193585 and VTT-E-213595. Because it is not clear that the properties of the strain are known and publicly available or can be reproducibly isolated from nature without undue experimentation and because the best mode disclosed by the specification requires the use of the bacterial strain, a suitable deposit for patent purposes is required.
If the deposit has been made under the provisions of the Budapest Treaty, filing of an affidavit or declaration by applicant or assignees or a statement by an attorney of record who has authority and control over the conditions of the deposit over his or her signature and registration number stating that the deposit has been accepted by an International Depository Authority under the provisions of the Budapest Treaty, that all restrictions upon public access to the deposit will be replaced if viable samples cannot be dispensed by the depository is required. This requirement is necessary when deposits are made under the provisions of the Budapest Treaty as the Treaty leaves this specific matter to the discretion of each State. Amendment of the specification to recite the date of the deposit and the complete name and full street address of the depository is required.
If the deposits have not been made under the provisions of the Budapest Treaty, then in order to certify that the deposits comply with the criteria set forth in 37 CFR §1.801-1.809, assurances regarding availability and permanency of deposits are required. Such assurance may be in the form of an affidavit or declaration by applicants or assignees or in the form of a statement by an attorney of record who has the authority and control over the conditions of deposit over his or her signature and registration number averring:
(a) during the pendency of this application, access to the deposits will be afforded to the Commissioner upon request;
(b) all restrictions upon the availability to the public of the deposited biological material will be irrevocably removed upon the granting of a patent on this application;
© the deposits will be maintained in a public depository for a period of at least thirty years from the date of the deposit or for the enforceable life of the patent or for a period of five years after the date of the most recent request for the furnishing of a sample of the deposited biological material, whichever is longest; and
(d) the deposits will be replaced if they should become non-viable or non-replicable.
In addition, a deposit of the biological material that is capable of self-replication either directly or indirectly must be viable at the time of the deposit and during the term of deposit. Viability may be tested by the depository. The test must conclude only that the deposited material is capable of reproduction. A viability statement for each deposit of a biological material not made under the Budapest Treaty must be filed in the application and must contain:
1)The name and address of the depository;
2)The name and address of the depositor;
3)The date of deposit;
4)The identity of the deposit and the accession number given by the depository;
5)The date of the viability test;
6)The procedures used to obtain a sample if the test is not done by the depository; and
7)A statement that the deposit is capable of reproduction.
If the deposit was made under the provisions of the Budapest Treaty, filing of an affidavit or declaration by Applicants, assignees or a statement by an attorney of record over his or her signature and registration number stating that deposit has been accepted by an International Depository Authority under the provisions of the Budapest Treaty, that all restrictions upon public access to the deposit will be irrevocably removed upon the grant of a patent on this application and that the deposit will be replaced if viable samples cannot be dispensed by the depository is required. This requirement is necessary when a deposit is made under the provisions of the Budapest Treaty as the Treaty leaves this specific matter to the discretion of each State. Amendment of the specification to recite the date of the deposit and the complete name and address of the depository is required.
As a possible means for completing the record, applicant may submit a copy of the contract with the depository for deposit and maintenance of each deposit.
If the deposit was made after the effective filing date of the application for patent in the United States, a verified statement is required from a person in a position to corroborate that the cell line described in the specification as filed is the same as that deposited in the depository. Corroboration may take the form of a showing of a chain of custody from applicant to the depository coupled with corroboration that the deposit is identical to the biological material described in the specification and in the applicant's possession at the time the application was filed.
Applicant's attention is directed to In re Lundak, 773 F.2d. 1216, 227 USPQ 90 (CAFC 1985) and 37 CFR §1.801-1.809 for further information concerning deposit practice.
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 1-6, 8 and 10 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter because the claims are drawn to bacteria which exist naturally in nature. Even though isolation structurally changes a nucleic acid from its natural state, the resultant difference is no enough to render the isolated bacteria different because the genetic structure has not been altered. The claim recites a “variant” of bacterial strain VTT-E-193585 comprising a genetic modification of one or more genes encoding PHA synthase which reduces the bacterial production of PHA; however, wild type genetic differences any strain of Xanthobacter bears in comparison to the deposited VTT-E-103585 and a cell cycle variation of the PHA production rate of the cell. The claim does not recite a transformed vector or a direct deletion mutation, etc., and a “genetic modification” can comprise natural mutations occurring in nature. With respect to claim 10, a “culture” is broad enough to read on the bacteria as found naturally in the seashore. The properties of claim 8 are inherent to the bacteria. See Myriad, 133 S.Ct. at 2166-18.
Claim Rejections - 35 USC § 112-2nd paragraph
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 1-6, 8 and 10 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.
Claims 1-8 and 10 are vague and indefinite because it the mere recitation of a name to describe the invention is not sufficient to satisfy the Statute's requirement of adequately describing and setting forth the inventive concept. The claim should provide any structural properties, such as the nucleic acid of the modified gene and the bacterial source (Genus/species) or the deposited variant strain number, which would allow for one to identify the strain without ambiguity. The mere recitation of a name, variant of bacterial strain VTT-E-193585 comprising a genetic modification of one or more genes encoding PHA, does not adequately define the claimed bacterial strain. Additionally, claim 8 recites a functional limitation but the strain has not been properly defined in any structural sense. Appropriate clarification and/or correction is required.
Claim 2 is vague and indefinite because it is unclear what the bacterial PHA synthase activity of strain VTT-E-193685 is since the strain is not adequately defined as described above. It is unclear how one would be able to make a comparison. Appropriate clarification and/or correction is required.
Claims 3-6 are vague and indefinite because the names phaC1 and phaC2 are not sufficient to describe the genes. it the mere recitation of a name to describe the invention is not sufficient to satisfy the Statute's requirement of adequately describing and setting forth the inventive concept. The claim should provide any structural properties, such as the nucleic acid of the genes, which would allow for one to identify the structures without ambiguity. Appropriate clarification and/or correction is required.
Claim Rejections - 35 USC § 112-Written description
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 1-6, 8 and 10 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 instant claims are drawn, for example, to:
A variant of bacterial strain VTT-E-193585 comprising a genetic modification of one or more genes encoding a PHA synthase that reduces the bacterial production of polyhydroxyalkanoic acid (PHA) as compared to strain VTT-E-193585.
The variant above, wherein the genetic modification reduces bacterial PHA synthase activity as compared to strain VTT-E-193585, preferably wherein PHA synthase activity has been reduced to less than 10%, such as less than 5%, for example less than 2%.
The variant above, wherein the variant comprises a genetic modification reducing the expression level of phaCl and/or the activity of the phaCl enzyme.
The variant according to claim 1, wherein the variant comprises a genetic modification reducing the expression level of phaC2 and/or the activity of the phaC2 enzyme.
wherein the variant has retained the ability to grow using hydrogen gas as energy source and carbon dioxide as the only carbon source.
The instant specification at the paragraph bridging pages 3-4 recites that strain VTT-E-193585 has been isolated from the seashore of the Baltic Sea in Naantali, Finland. This organism is able to grow in suitable bioreactor conditions with minimal mineral medium with hydrogen as the energy source and carbon dioxide as the carbon source at limited oxygen conditions. 16S sequencing and Illumina metagenomics sequencing have shown that the strain most likely is a member of the genus, member of the genus Xanthobacter, but species is not known.
The inventors have constructed genetically-modified variants of VTT-E-193585 comprising disruptions of the phaC1 and/or phaC2 loci. The variant comprising a gene disruption of phaC1 has been deposited on April 19th, 2021 in the VTT Culture Collection at the VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Finland, an International Depositary Authority under the Budapest Treaty. The accession number is VTT E-213595.
In a first main aspect, the invention relates to a variant of bacterial strain VTT-E-193585 comprising a genetic modification that reduces the bacterial production of polyhydroxyalkanoic acid (PHA) as compared to strain VTT-E-193585. Thus, the invention relates to a genetically-modified variant of bacterial strain VTT-E-193585. In other words, strain VTT-E-193585 further characterized in that it comprises a genetic modification. Page 5 of the specification recites that the variant is the bacterial strain deposited under number VTT-E-213595, in which the phaC1 gene has been disrupted. In a preferred embodiment, the variant has retained the ability to grow using hydrogen gas as energy source and carbon dioxide as the only carbon source. In one embodiment, if the strain is a variant of strain VTT-E-193585, the variant comprises the 16S ribosomal RNA set forth in SEQ ID NO:1 or a 16S ribosomal RNA having up to 20 nucleotide differences with SEQ ID NO:1, e.g. 1 to 10, such as 1 to 5, e.g. one, two or three nucleotide differences with SEQ ID NO:1.
Page 52 of the instant specification recites that the sequencing of the bacterial genome of strain VTT-E-193585 described in Example 1 identified genes phaC1 (SEQ ID NO:60, encoding the protein set forth in SEQ ID NO:62) and phaC2 (SEQ ID NO:61, encoding the protein set forth in SEQ ID NO:63). Two plasmids were constructed to target deletion of phaC1 and phaC2 genes in the genome of SoF1 (Table 7).
Accordingly, the instant specification does not provide written description for the full breadth of the claims.
To fulfill the written description requirements set forth under 35 USC § 112, first paragraph, the specification must describe at least a substantial number of the members of the claimed genus, or alternatively describe a representative member of the claimed genus, which shares a particularly defining feature common to at least a substantial number of the members of the claimed genus, which would enable the skilled artisan to immediately recognize and distinguish its members from others, so as to reasonably convey to the skilled artisan that Applicant has possession the claimed invention. Applicants have not described the genus of claimed fructanases such that the specification might reasonably convey to the skilled artisan that Applicants had possession of the claimed invention at the time the application was filed.
The description in the claims allows for many different bacterial strains found in from many different sources with PHA genes not disclosed in the instant specification and/or well-known in the prior art.
With the written description of a genus, however, merely drawing a fence around a perceived genus is not a description of the genus. One needs to show that one has truly invented the genus, i.e., that one has conceived and described sufficient representative species encompassing the breadth of the genus. Otherwise, one has only a research plan, leaving it to others to explore the unknown contours of the claimed genus. See Ariad, 598 F.3d at 1353 (The written description requirement guards against claims that "merely recite a description of the problem to be solved while claiming all solutions to it and . . . cover any compound later actually invented and determined to fall within the claim's functional boundaries."). Abbvie Deutschland GmbH & Co. v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 U.S.P.Q.2d 1780, 1790, 2014 BL 183329, 12 (Fed. Cir. 2014).
To fulfill the written description requirements set forth under 35 USC § 112, first paragraph, the specification must describe at least a substantial number of the members of the claimed genus, or alternatively describe a representative member of the claimed genus, which shares a particularly defining feature common to at least a substantial number of the members of the claimed genus, which would enable the skilled artisan to immediately recognize and distinguish its members from others, so as to reasonably convey to the skilled artisan that Applicant has possession the claimed invention. Applicants have not described the genus of variants of VTT-E-193585 with one or more genetic modifications in one of more genes encoding a PHA synthase such that the specification might reasonably convey to the skilled artisan that Applicants had possession of the claimed invention at the time the application was filed.
The purpose of the "written description" requirement is broader than tomerely explain how to "make and use"; the applicant must convey with reasonableclarity to those skilled in the art that, as of the filing date sought, he or she was inpossession of the invention. The invention is, for purposes of the "writtendescription" inquiry, whatever is now claimed. See Vas-Cath, Inc. v. Mahurkar,935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Federal Circuit, 1991).Furthermore, the written description provision of 35 USC § 112 is severable fromits enablement provision; and adequate written description requires more than amere statement that it is part of the invention and reference to a potential methodfor isolating it. The nucleic acid [product] itself is required. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (CAFC 1993) and Amgen Inc. V. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016. Possession may be shown in a variety of ways including description of an actual reduction to practice, or by showing the invention was 'ready for patenting' such as by disclosure of drawings or structural chemical formulas that show that the invention was complete, or by describing distinguishing identifying characteristics sufficient to show that the applicant was in possession of the claimed invention" (Id. at 1104). Moreover, because the claims encompass a genus of variant species, an adequate written description of the claimed invention must include sufficient description of at least a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics sufficient to show that Applicant was in possession of the claimed genus. An objective standard for determining compliance with the written description requirement is, "does the description clearly allow persons of ordinary skill in the art to recognize that he or she invented what is claimed." In re Gosteli, 872 F.2d 1008, 1012, 10 USPQ2d 1614, 1618 (Fed. Cir. 1989). To satisfy the written description requirement, an 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, and that the invention, in that context, is whatever is now claimed. Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Fed. Cir. 1991) and MPEP 2163.02.
However, factual evidence of an actual reduction to practice has not been disclosed by Applicant in the specification with the exception of the deposited variant VTT-E-21395; and with a VTT-E-193585 strain with a mutation in phaC1 comprising SEQ ID NO: 60 and/or phaC2 comprising SEQ ID NO: 61 wherein the mutation reduces the strains production of PHA as compared to wild-type VTT-E-21395. Applicant has not shown the invention was "ready for patenting" by disclosure of drawings or structural chemical formulas that show that the invention was complete; nor has Applicant described distinguishing identifying characteristics sufficient to show that Applicant were in possession of the claimed invention at the time the application was filed. For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus'" (Id. at 1106); accordingly, it follows that an adequate written description of a genus cannot be achieved in the absence of a disclosure of at least one species within the genus. The scope of the claim includes numerous structural variants, and the genus is highly variant because a significant number of structural differences between genus members is permitted.
One of skill in the art would reasonably conclude that the disclosure fails to provide a representative number of species to describe the genus, and thus, that the applicant was not in possession of the claimed genus. The claimed subject matter is not supported by an adequate written description because a representative number of species has not been described.
Because the art is unpredictable, in accordance with the Written Description Guidelines and the scope of the claim includes numerous structural variants and the genus is highly variant because a significant number of structural differences between genus members is permitted. The specification does not describe any members of the claimed genus by complete structure. One of skill in the art would reasonably conclude that the disclosure fails to provide a representative number of species to describe the genus, and thus, that the applicant was not in possession of the claimed genus. The claimed subject matter is not supported by an adequate written description because a representative number of species has not been described.
There are no drawings or structural formulas disclosed of any of theseother bacteria and other PHA sequences with the recited functional requirements. Based on the lack of knowledge and predictability in the art, those of ordinaryskill in the art would not conclude that the applicant was in possession of theclaimed genus of bacterial variant strains.
Applicant is referred to the revised guidelines concerning compliance with the written description requirement of U.S.C. 112, first paragraph, published in the Official Gazette and also available at www.uspto.gov
Claim Rejections - 35 USC § 112-Scope of Enablement
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 1-6, 8 and 10 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for:
The bacterial strain deposited under VTT-E-213595 which comprises a genetic modification in the phaC1 gene comprising SEQ ID NO: 60 which reduces the bacterial production of polyhydroxyalkanoic acid (PHA); and/or
A variant of deposited bacterial strain VTT-E-193585 wherein said variant has a genetic mutation in the phaC1 gene comprising SEQ ID NO: 60 that reduces its production of polyhydroxyalkanoic acid (PHA),
does not reasonably provide enablement for:
A variant of bacterial strain VTT-E-193585 comprising a genetic modification of one or more genes encoding a PHA synthase that reduces the bacterial production of polyhydroxyalkanoic acid (PHA) as compared to strain VTT-E-193585.
The variant above, wherein the genetic modification reduces bacterial PHA synthase activity as compared to strain VTT-E-193585, preferably wherein PHA synthase activity has been reduced to less than 10%, such as less than 5%, for example less than 2%.
wherein the variant has retained the ability to grow using hydrogen gas as energy source and carbon dioxide as the only carbon source.
The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
The specification states that substitutions, additions, or deletions, may be made to the defined sequences; however, the specification provides no guidance as which amino acids may be changed without causing a detrimental effect to the enzyme and with the added enzymatic function requirement. It is unpredictable as to which amino acids could be removed and which could be added. While it is known that many amino acid substitutions are possible in any given protein, the position within the protein’s sequence where amino acid substitutions can be made with a reasonable expectation of success are limited. Other positions are critical to the protein’s structure/function relationship, e.g., such as various positions or regions directly involved in binding, catalysis in providing the correct three-dimensional spatial orientation of binding and catalytic sites. These regions can tolerate only very little or no substitutions. Selective point mutation to one key residue could eliminate the function of the polypeptide. It could eliminate its functional properties. If the range of decreased binding ability after single point mutation of a protein antigen varies, one could expect point mutations in the protein antigen to cause varying degrees of loss of protection/function, depending on the relative importance to the binding interaction of the altered residue. Alternatively, the combined effects of multiple changes, as instantly claimed, in an antigenic determinant could again result in loss of function. A protein having multiple point mutations, or accumulated point mutations at key residues could create a new antigen that is precipitously or progressively unrecognizable. As stated above, Applicants have not shown the particular substitution and the result it produces. Applicants have provided no guidance to enable one of ordinary skill in the art how to determine, without undue experimentation, the effects of different amino substitutions and the nature and extent of the changes that can be made. It is expensive and time consuming to make amino acid substitutions at more than one position, in a particular region of the protein, in view of the many fold possibilities for change in structure and the uncertainty as to what utility will be possessed. See Mikayama et al. (Nov.1993. Proc.Natl.Acad.Sci. USA, vol. 90 : 10056-10060) which teaches that the three-dimensional structure of molecules is important for their biological function and even a single amino acid difference may account for markedly different biological activities. Amino acids owe their ‘significance’ to their inclusion in a pattern which is directly involved in recognition by, and binding to, the receptor and the significance of the particular amino acids and sequences for different amino acids cannot be predicted a priori, but must be determined from case to case by painstaking experimental study. The instant claims allow for substitutions with amino acids of vastly different properties and they do not recite the specific changes in the claims.
Applicants have recited that in the instant specification at the paragraph bridging pages 3-4 recites that strain VTT-E-193585 has been isolated from the seashore of the Baltic Sea in Naantali, Finland. This organism is able to grow in suitable bioreactor conditions with minimal mineral medium with hydrogen as the energy source and carbon dioxide as the carbon source at limited oxygen conditions. 16S sequencing and Illumina metagenomics sequencing have shown that the strain most likely is a member of the genus, member of the genus Xanthobacter, but species is not known.
The inventors have constructed genetically-modified variants of VTT-E-193585 comprising disruptions of the phaC1 and/or phaC2 loci. The variant comprising a gene disruption of phaC1 has been deposited on April 19th, 2021 in the VTT Culture Collection at the VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Finland, an International Depositary Authority under the Budapest Treaty. The accession number is VTT E-213595.
In a first main aspect, the invention relates to a variant of bacterial strain VTT-E-193585 comprising a genetic modification that reduces the bacterial production of polyhydroxyalkanoic acid (PHA) as compared to strain VTT-E-193585. Thus, the invention relates to a genetically-modified variant of bacterial strain VTT-E-193585. In other words, strain VTT-E-193585 further characterized in that it comprises a genetic modification. Page 5 of the specification recites that the variant is the bacterial strain deposited under number VTT-E-213595, in which the phaC1 gene has been disrupted. In a preferred embodiment, the variant has retained the ability to grow using hydrogen gas as energy source and carbon dioxide as the only carbon source. In one embodiment, if the strain is a variant of strain VTT-E-193585, the variant comprises the 16S ribosomal RNA set forth in SEQ ID NO:1 or a 16S ribosomal RNA having up to 20 nucleotide differences with SEQ ID NO:1, e.g. 1 to 10, such as 1 to 5, e.g. one, two or three nucleotide differences with SEQ ID NO:1.
Page 52 of the instant specification recites that the sequencing of the bacterial genome of strain VTT-E-193585 described in Example 1 identified genes phaC1 (SEQ ID NO:60, encoding the protein set forth in SEQ ID NO:62) and phaC2 (SEQ ID NO:61, encoding the protein set forth in SEQ ID NO:63). Two plasmids were constructed to target deletion of phaC1 and phaC2 genes in the genome of SoF1 (Table 7).
The scope of the claim includes numerous structural variants, and the genus is highly variant because a significant number of structural differences between genus members is permitted. The specification fails to teach other variants of bacterial strain VTT-E-193585 in such the term “variant” allows for bacterial of many different Genus and species and the claim fails to teach other bacteria that are of the same Genus species of VTT-E-193585, and the working examples only show the variant is the bacterial strain deposited under number VTT-E-213595, in which the phaC1 gene has been disrupted. in Example 1 identified genes phaC1 (SEQ ID NO:60, encoding the protein set forth in SEQ ID NO:62) and phaC2 (SEQ ID NO:61, encoding the protein set forth in SEQ ID NO:63) only.
Genentech Inc. v. Novo Nordisk A/S (CAFC) 42 USPQ2d 1001 clearly states: “Patent protection is granted in return for an enabling disclosure of an invention, not for vague intimations of general ideas that may or may not be workable. See Brenner v. Manson, 383 U.S. 519, 536, 148 USPQ 689, 696 (1966) (stating, in context of the utility requirement, that "a patent is not a hunting license. It is not a reward for the search, but compensation for its successful conclusion.") Tossing out the mere germ of an idea does not constitute enabling disclosure. While every aspect of a generic claim certainly need not have been carried out by an inventor, or exemplified in the specification, reasonable detail must be provided in order to enable members of the public to understand and carry out the invention.”
The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these 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.
Claim(s) 1-6, 8 and 10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Reed et al (WO 2017/165244 A1; September 28, 2017; provided by Applicants) Pearlman et al (US20190124947 A1; 5/2/2019) and Feinberg et al (US 2020/224236 A1; July 16, 2020; provided by Applicants).
NOTE: The paragraph bridging pages 3-4 of the instant specification recites: Strain VTT-E-193585 has been isolated from the seashore of the Baltic Sea in Naantali, Finland. This organism is able to grow in suitable bioreactor conditions with minimal mineral medium with hydrogen as the energy source and carbon dioxide as the carbon source at limited oxygen conditions. 16S sequencing and Illumina metagenomics sequencing have shown that the strain most likely is a member of the genus, member of the genus Xanthobacter, but species is not known. The claims are drawn to variants of this strain.
Reed et al discloses Xanthobacter autotrophicus grown under chemoautotrophic conditions as recited in instant claim 8 (CO2 as sole carbon source and H2 as source of energy) for the production of high protein biomass. The cells were cultured at 30 degrees, 64%H2, 11% CO2 and 5,4% O2 at pH 6,8. Biomass was pelleted and freeze dried (see example 14 paragraphs 424-429). However, Reed does not explicitly recite that there is a genetic modification in one or more genes encoding PHA, yet it has the same growth conditions as the variant instantly claimed (instant claim 8).
The teachings of Feinberg and Pearlman teach that PHB was undesirable in chemoautrophic bacteria and teach the disruption/modification or deletion of the PHB genes (these include the phaC genes), and more particularly in phaC1 and phaC2 as described below.
Feinberg et al discloses chemoautotroph bacteria Methylobacterium extorquens having a deletion of PHB biosynthesis enzymes ( e.g. Mext_2223) results in a dramatic decrease in PHB production (See FIG. 2B and paragraph 181). Decreasing PHB production was shown to increase protein content in cells (see figs. 6A and 6B, paragraph 189). Xanthobacter is claimed as an alternative. The difference with the teachings of Reed lies in the disruption of PHA synthase gene. The technical effect associated with the difference consist of a decrease in PHB production. The negative correlation between cell growth and PHB production in chemoautotrophs was already known in the prior art from Feinberg. Accordingly, it would have been prima facie obvious to one of ordinary skill in the art to combine Reed and Feinberg to produce a variant bacterial strain with reduced producing of polyhydroxyalkanoic acid (PHA) as compared to a wild-type strain.
Additionally, Pearlman et al teach a chemoautotrophic bacterial strain comprising a genetic modification that reduces the bacterial production of PHA. See, for example, paragraphs [0029]-[0031]; examples 1 and 9, C. necator H16 AphaCAB and H16 PHB4 strains. PHB falls within the broader class of polyhydroxyalkanoates (PHAs), which are key intracellular carbon and energy storage compounds enabling a large number of prokaryotic cell types to survive periods of starvation and other stressful conditions. At para [006] paragraph teaches PHA polymer is poly(3-hydroxybutyrate) (PHB) which is rarely digestible and offers little to no nutritional value. The PHB component also reduces the protein content of the organism. In addition, non-nutritive PHB storage compound in the cytoplasm takes up physical space, leaving less space for nutritive compounds. Further, in some instances, the PHB components had a detrimental impact on biological functions, such as digestive system processes. Pearlman teaches at para. [0029] In one nonlimiting embodiment, PHB production in the organism is attenuated or eliminated by modifying one or more of the phaCAB operon enzymes which enable the strain to produce PHB. In one nonlimiting embodiment, the organism is a ΔphaCAB H16 C. necator strain. In one nonlimiting embodiment, the organism is a PHB-strain. In one nonlimiting embodiment, the PHB-strain is produced by a G320A point mutation in phaC. In paragraph [0030] By phaCAB operon enzymes it is meant to include enzymes phaA, phaB, and phaC. In one nonlimiting embodiment, the organism has at least one modification of one or more of the phaCAB operon enzymes excluding a phasin modification. By “modify”, “modifying” or “modification”, as used herein it is meant to include gene deletion, gene substitution or gene insertion in one or more genes encoding phaA, phaB or phaC. Various methods for modification can be used.
Para. [0031] In one nonlimiting embodiment, modification is carried out by allele exchange. In this embodiment, genome edits are made in an organism such as C. necator by allele exchange (also referred to as allelic exchange). In one nonlimiting embodiment, the organism is a ΔphaCAB H16 C. necator strain generated using allele exchange. Para. [0012] In one nonlimiting embodiment, the organism of the nutritive composition does not comprise an exogenous nucleic acid. In one nonlimiting embodiment, the organism of the nutritive composition has at least one modification of one or more of the phaCAB operon enzymes excluding a phasin modification. In one nonlimiting embodiment, PHB production in the organism is attenuated or eliminated by eliminating or attenuating activity of one or more phaCAB operon enzymes excluding a phasin modification. In one nonlimiting embodiment, the organism of the nutritive composition is Cupriavidus necator. In one nonlimiting embodiment, the organism of the nutritive composition having attenuated PHB production produces undetectable PHB.
It is noted that the term "comprises a genetic modification that reduces [...] PHA" of claim 1 does not disregard wild type genetic differences any strain of Xanthobacter bears in comparison to the deposited VTT-E-193585 and a cell cycle variation of the PHA production rate of the cell. Reading into the claims a deliberate gene mutation introduced by man, it would have been obvious to mutate a bacterium, particularly Xanthobacter as disclosed in Reed and Feinberg, to reduce the production of PHA from the bacterial cells because both Feinberg and Pearlman teach PHA polymer is poly(3-hydroxybutyrate) (PHB) which is rarely digestible and offers little to no nutritional value. The PHB component also reduces the protein content of the organism. In addition, non-nutritive PHB storage compound in the cytoplasm takes up physical space, leaving less space for nutritive compounds. Further, in some instances, the PHB components had a detrimental impact on biological functions, such as digestive system processes. Pearlman teaches at para. PHB production in the organism is attenuated or eliminated by modifying one or more of the phaCAB operon enzymes which enable the strain to produce PHB. The chemoautotrophic bacteria in the prior art references are considered “variants of VTT-E-193585.
Prior art, not presently relied upon:
TITLE: Studies on polyhydroxyalkanoate (PHA) accumulation
in a PHA synthase I-negative mutant of Burkholderia
cepacia generated by homogenotization
AUTHOR(S): de Andrade Rodrigues, M. F.; Vicente, E. J.;
Steinbuchel, A.
CORPORATE SOURCE: Instituto de Pesquisas Technologicas do Estado de Sao
Paulo, Sao Paulo, Brazil
SOURCE: FEMS Microbiology Letters (2000), 193(1), 179-185
CODEN: FMLED7; ISSN: 0378-1097
DIGITAL OBJECT ID: 10.1016/S0378-1097(00)00483-3
PUBLISHER: Elsevier Science B.V.
DOCUMENT TYPE: Journal
LANGUAGE: English
ED Entered STN: 29 Nov 2000
AB In the genome of Burkholderia cepacia strain IPT64, which accumulates a
blend of the two homopolyesters poly(3-hydroxybutyrate) [poly(3HB)] and
poly(3-hydroxy-4-pentenoic acid) [poly(3H4PE)] from sucrose or gluconate
as single carbon source, the polyhydroxyalkanoate (PHA) synthase
structural gene was disrupted by the insertion of a
chloramphenicol-resistant gene cassette (phaC1::Cm). The suicide vector
pSUP202 harboring phaC1::Cm was transferred to B. cepacia by
conjugation. The inactivated gene was integrated into the chromosome of
B. cepacia by homologous recombination. This mutant and also 15
N-methyl-N'-nitrosoguanidine (NMG)-induced mutants still accumulated low
amts. of PHAs and expressed low PHA synthase activity. The anal. of the
mutant phaC1::Cm showed that it accumulated about 1% of PHA consisting
of 68.2 mol% 3HB and 31.8 mol% 3H4PE from gluconate. The wild-type, in
contrast, accumulated 49.3% of PHA consisting of 96.5 mol% 3HB and 3.5
mol% 3H4PE. Our results indicated that the genome of B. cepacia possesses
at least two PHA synthase genes, which probably have different substrate
specificities.
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/JENNIFER E GRASER/ Primary Examiner, Art Unit 1645 2/20/26