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
Amended Claims 34-48 (dated 05/28/2025) are pending in this application and are now under consideration for examination.
Priority
Acknowledgment is also made of applicants’ claim for foreign priority under 35 U.S.C. 119(a)-(d). This application is a 371 of PCT/EP2023/059268 filed on 04/06/2023 and claims the priority date of EPO Application 22382336.0 filed on 04/07/2022.
Information disclosure statement
The information disclosure statements (IDS) submitted on 10/24/2024, 10/28/2024, 05/28/2025 and 06/26/2025 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS statements are considered and initialed by the examiner.
Duty to Disclose
Examiner notes that there are a number of applications filed by the assignee/inventors of this instant application wherein said applications are drawn to a biodegrading, or oxidizing and/or depolymerizing polyolefin. Examiner would like to reiterate to applicants’, that it is their duty to disclose to the examiner any or all applications and allowed patents that either claims the same subject matter or related subject matter and those that are material to the prosecution of this instant application, such that double patenting can be avoided. Examiner urges the applicants’ to provide a list of their conflicting/related applications, identical to that claimed herein and a list of claims filed in other applications and take steps at their end to avoid double patenting.
Claims Objections
Claim 34 and claims 35-48 depending therefrom are objected; Recitation of “and/or” in claims 34, 42, 45 and 47-48 makes the claim indefinite, as it is not clear what limitations must be present. Correction and clarification is required. Examiner suggests amending the claim to recite “…or …”.
Claim Rejections: 35 USC § 112(b)
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.
I. Claim 34 and claims 35-48 depending therefrom 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; recitation of “and/or” in claims 34, 42, 45 and 47-48 makes the claims indefinite, as it is not clear what limitations must be present. The metes and bounds of claims 34, 42, 45 and 47-48 is not clear and thus, it would not be possible to one of ordinary skill in the art to define the metes and bounds of the desired patent protection. The rejection may be overcome by amending the claims to recite “… or …”. Correction and clarification is required. Examiner suggests amending the claim to recite “…or …”.
II. Claim 39 is rejected under of 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 applicant regards as the invention.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) is considered indefinite, since the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). Note the explanation given by the Board of Patent Appeals and Interferences in Ex parte Wu, 10 USPQ2d 2031, 2033 (Bd. Pat. App. & Inter. 1989), as to where broad language is followed by "such as" and then narrow language. The Board stated that this can render a claim indefinite by raising a question or doubt as to whether the feature introduced by such language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. Note also, for example, the decisions of Ex parte Steigewald, 131 USPQ 74 (Bd. App. 1961); Ex parte Hall, 83 USPQ 38 (Bd. App. 1948); and Ex parte Hasche, 86 USPQ 481 (Bd. App. 1949).
In the present instance, claim 39 recites the broad recitation has at least 80% sequence identity to SEQ ID NO:2 …” and the claim also recite “… at least …98% or 99%…”, which is the narrower statement of the sequence identity range/limitation (range within range). It is not clear what the applicants’ intend to encompass in the rejected claims and the metes and bounds of the claims are unclear and as being indefinite, since the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. Correction and clarification is required. Examiner suggests for the following sequence identities “… at least 85% … 98% or at least 99% …” applicants’ consider writing additional new claims as dependent claims.
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.
Claim 48 is rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more. Claim(s) 48 is/are directed to a natural phenomenon. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception for the reasons stated below.
MPEP 2106(III) directs that claims drawn to 1) a composition of matter (step 1), 2) a law of nature or a natural phenomenon or a product of nature (step 2A) and 3) lacking recitation of additional elements that make the claims directed to significantly more than a judicial exception (step 2B) are ineligible for patenting under 35 U.S.C. 101. See MPEP 2106(III), flow chart.
“If the claim includes a nature-based product that does not exhibit markedly different characteristics from its naturally occurring counterpart in its natural state, then the claim is directed to a ‘product of nature’ exception (Step 2A: YES), and requires further analysis in Step 2B to determine whether any additional elements in the claim add significantly more to the exception.” MPEP 2106.04(c). “It is important to keep in mind that product of nature exceptions include both naturally occurring products and non-naturally occurring products that lack markedly different characteristics from any naturally occurring counterpart.” MPEP 2106.04(b)(II). “The markedly different characteristics analysis compares the nature-based product limitation to its naturally occurring counterpart in its natural state. Markedly different characteristics can be expressed as the product’s structure, function, and/or other properties, and are evaluated based on what is recited in the claim on a case-by-case basis. If the analysis indicates that a nature-based product limitation does not exhibit markedly different characteristics, then that limitation is a product of nature exception. If the analysis indicates that a nature-based product limitation does have markedly different characteristics, then that limitation is not a product of nature exception. Examiners should keep in mind that if the nature-based product limitation is naturally occurring, there is no need to perform the markedly different characteristics analysis because the limitation is by definition directed to a naturally occurring product and thus falls under the product of nature exception.”
Here, claim 48 is directed towards a composition of matter i.e., “a) an isolated enzyme comprising an amino acid sequence having an amino acid sequence identity of at least 75% with SEQ ID NO: 1,... or c) a composition comprising said isolated enzyme or…”. As discussed above, the following sequence alignment discloses the following (see provided sequence alignment): NCBI Reference Sequence XP_026756396.1, discloses a naturally-occurring arylphorin subunit alpha-like protein obtained from Galleria mellonella having 100% sequence identity to SEQ ID NO: 1 of the instant invention. Since claim 48 encompass at least one naturally-occurring protein/enzyme, for step 2A “there is no need to perform the markedly different characteristics analysis because the limitation is by definition directed to a naturally occurring product and thus falls under the product of nature exception.” Regarding Step 2B for claim 48 “Step 2B asks: Does the claim recite additional elements that amount to significantly more than the judicial exception”? MPEP 2106.05(II). Here, claims 48 does not recite any additional elements other than “a) an isolated enzyme comprising an amino acid sequence having an amino acid sequence identity of at least 75% with SEQ ID NO: 1,... or c) a composition comprising said isolated enzyme or…” that encompasses natural products. As such, Step 2B is answered in the negative and claim 48 is directed towards a judicial exception.
Regarding claim 48 is also directed towards compositions of matter. Claim 48 recites the same product of nature as present in a man-made composition (or potentially man-made composition). “When a claim recites a nature-based product limitation, examiners should use the markedly different characteristics analysis discussed in MPEP § 2106.04(c) to evaluate the nature-based product limitation and determine the answer to Step 2A.” MPEP 2106.04(b)(II). “Where the claim is to a nature-based product produced by combining multiple components (e.g., a claim to "a probiotic composition comprising a mixture of Lactobacillus and milk"), the markedly different characteristics analysis should be applied to the resultant nature-based combination, rather than its component parts.” MPEP 2106.04(c)(I)(A). “Where the claim is to a nature-based product in combination with non-nature based elements (e.g., a claim to "a yogurt starter kit comprising Lactobacillus in a container with instructions for culturing Lactobacillus with milk to produce yogurt"), the markedly different characteristics analysis should be applied only to the nature-based product limitation.” MPEP 2106.04(c)(I)(A).
“The courts have emphasized that to show a marked difference, a characteristic must be changed as compared to nature, and cannot be an inherent or innate characteristic of the naturally occurring counterpart or an incidental change in a characteristic of the naturally occurring counterpart. Myriad, 133 S. Ct. at 2111, 106 USPQ2d at 1974-75. Thus, in order to be markedly different, applicant must have caused the claimed product to possess at least one characteristic that is different from that of the counterpart.” MPEP 2106(c)(II)(C). Here, there is no evidence of record that indicates that placement of the naturally-occurring polypeptide i.e., NCBI Reference Sequence XP_026756396.1, discloses a naturally-occurring arylphorin subunit alpha-like protein obtained from Galleria mellonella having 100% sequence identity to SEQ ID NO: 1 of the instant invention composition in a kit as recited in claim 48 introduces any specific characteristic that is not an inherent or innate characteristic of the naturally-occurring counterpart or an incidental change in a characteristic of the naturally occurring counterpart arylphorin subunit alpha-like obtained from Galleria mellonella having 100% sequence identity to SEQ ID NO: 1 (e.g. physical form as in a kit etc., is an incidental change in characteristic). As such, regarding claim 48, the recited composition in a kit does not appear to possess a marked difference such that Step 2A is answered as the composition of claim 48 not being markedly different. As such, claim 48 is directed towards a judicial exception for the reasons set forth above.
Claim Rejections: 35 USC § 112(a)
The following is a quotation 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.
Written Description
I. Claims 34-48 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112, first paragraph, as containing 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(s), at the time the application was filed, had possession of the claimed invention.
Claims 34-48 of the instant application as interpreted are directed to a method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, comprising contacting: any enzyme capable of biodegrading, or oxidizing and/or depolymerizing a polyolefin-derived polymer including variants, mutants and homologs…, said enzyme having an amino acid sequence identity of at least 75% with SEQ ID NO: 1… (as in claims 34-37, 41-42 and 46-47); an expression vector comprising encoding nucleotide sequence, host cell comprising said expression vector and a method of expressing said encoded enzyme (as in claims 42-44) and a kit/composition comprising said enzyme (as in claim 48); and said method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, further comprising any second enzyme of undefined activity which comprises an amino acid sequence having an amino acid sequence identity of at least 75% with SEQ ID NO: 2 including variants, mutants and homologs (as in claims 38-40; also see claims objections and 35 U.S.C. 112(b) rejection above for claim interpretation).
In University of California v. Eli Lilly & Co., 43 USPQ2d 1938, the Court of Appeals for the Federal Circuit has held that “A written description of an invention involving a chemical genus, like a description of a chemical species, ‘requires a precise definition, such as by structure, formula, [or] chemical name,’ of the claimed subject matter sufficient to distinguish it from other materials”. As indicated in MPEP § 2163, 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 that Applicant was in possession of the claimed genus. In addition, MPEP § 2163 states that 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.
In the instant case, there is no structure associated with function with regard to the members of the genus of polypeptides and encoding polynucleotides i.e., a method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, comprising contacting: any enzyme capable of biodegrading, or oxidizing and/or depolymerizing a polyolefin-derived polymer including variants, mutants and homologs…, said enzyme having an amino acid sequence identity of at least 75% with SEQ ID NO: 1… (as in claims 34-37, 41-42 and 46-47); an expression vector comprising encoding nucleotide sequence, host cell comprising said expression vector and a method of expressing said encoded enzyme (as in claims 42-44) and a kit/composition comprising said enzyme (as in claim 48); and said method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, further comprising any second enzyme of undefined activity which comprises an amino acid sequence having an amino acid sequence identity of at least 75% with SEQ ID NO: 2 including variants, mutants and homologs (as in claims 38-40; also see claims objections and 35 U.S.C. 112(b) rejection above for claim interpretation).
No information, beyond the characterization of two species: polypeptides comprising the amino acid sequences of SEQ ID NO: 1 and SEQ ID NO: 2 and capable of biodegrading, or oxidizing and/or depolymerizing a polyolefin-derived polymer, has been provided by the applicants’ in the claimed method and composition, which would indicate that they had possession of the claimed genus of polypeptides and encoding polynucleotides i.e., a method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, comprising contacting: any enzyme capable of biodegrading, or oxidizing and/or depolymerizing a polyolefin-derived polymer including variants, mutants and homologs…, said enzyme having an amino acid sequence identity of at least 75% with SEQ ID NO: 1… (as in claims 34-37, 41-42 and 46-47); an expression vector comprising encoding nucleotide sequence, host cell comprising said expression vector and a method of expressing said encoded enzyme (as in claims 42-44) and a kit/composition comprising said enzyme (as in claim 48); and said method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, further comprising any second enzyme of undefined activity which comprises an amino acid sequence having an amino acid sequence identity of at least 75% with SEQ ID NO: 2 including variants, mutants and homologs (as in claims 38-40; also see claims objections and 35 U.S.C. 112(b) rejection above for claim interpretation).
The genus of polypeptides and the encoding polynucleotides required in the claimed invention is an extremely large structurally and functionally variable genus. While the argument can be made that the recited genus of polypeptides is adequately described by the disclosure of the structures of SEQ ID NO: 1 and SEQ ID NO: 2 with specific structures having the claimed associated function/activity, since one could use structural homology to isolate those polypeptides and the encoding polynucleotides recited in the claims. The art clearly teaches the “Practical Limits of Function Prediction”: (a) Devos et al., (Proteins: Structure, Function and Genetics, 2000, Vol. 41: 98-107), teach that the results obtained by analyzing a significant number of true sequence similarities, derived directly from structural alignments, point to the complexity of function prediction. Different aspects of protein function, including (i) enzymatic function classification, (ii) functional annotations in the form of key words, (iii) classes of cellular function, and (iv) conservation of binding sites can only be reliably transferred between similar sequences to a modest degree. The reason for this difficulty is a combination of the unavoidable database inaccuracies and plasticity of proteins (Abstract, page 98) and the analysis poses interesting questions about the reliability of current function prediction exercises and the intrinsic limitation of protein function prediction (Column 1, paragraph 3, page 99) and conclude that “Despite widespread use of database searching techniques followed by function inference as standard procedures in Bioinformatics, the results presented here illustrate that transfer of function between similar sequences involves more difficulties than commonly believed. Our data show that even true pair-wise sequence relations, identified by their structural similarity, correspond in many cases to different functions (column 2, paragraph 2, page 105).
(b) Whisstock et al., (Quarterly Reviews of Biophysics 2003, Vol. 36 (3): 307-340) also highlight the difficulties associated with “Prediction of protein function from protein sequence and structure”; “To reason from sequence and structure to function is to step onto much shakier ground”, closely related proteins can change function, either through divergence to a related function or by recruitment for a very different function, in such cases, assignment of function on the basis of homology, in the absence of direct experimental evidence, will give the wrong answer (page 309, paragraph 4), it is difficult to state criteria for successful prediction of function, since function is in principle a fuzzy concept. Given three sequences, it is possible to decide which of the three possible pairs is most closely related. Given three structures, methods are also available to measure and compare similarity of the pairs. However, in many cases, given three protein functions, it would be more difficult to choose the pair with most similar function, although it is possible to define metrics for quantitative comparisons of different protein sequences and structures, this is more difficult for proteins of different functions (page 312, paragraph 5), in families of closely related proteins, mutations usually conserve function but modulate specificity i.e., mutations tend to leave the backbone conformation of the pocket unchanged but to affect the shape and charge of its lining, altering specificity (page 313, paragraph 4), although the hope is that highly similar proteins will share similar functions, substitutions of a single, critically placed amino acid in an active-site residue may be sufficient to alter a protein’s role fundamentally (page 323, paragraph 1).
(c) This finding is reinforced in the following scientific teachings for specific proteins in the art that suggest, even highly structurally homologous polynucleotides and encoded polypeptides do not necessarily share the same function. For example, Witkowski et al., (Biochemistry 38:11643-11650, 1999), teaches that one conservative amino acid substitution transforms a -ketoacyl synthase into a malonyl decarboxylase and completely eliminates -ketoacyl synthase activity. Seffernick et al., (J. Bacteriol. 183(8): 2405-2410, 2001), teaches that two naturally occurring Pseudomonas enzymes having 98% amino acid sequence identity catalyze two different reactions: deamination and dehalogenation, therefore having different function. Broun et al., (Science 282:1315-1317, 1998), teaches that as few as four amino acid substitutions can convert an oleate 12-desaturase into a hydrolase and as few as six amino acid substitutions can transform a hydrolase to a desaturase.
As stated above, no information beyond the characterization of two species: polypeptides comprising the amino acid sequences of SEQ ID NO: 1 and SEQ ID NO: 2 and capable of biodegrading, or oxidizing and/or depolymerizing a polyolefin-derived polymer, has been provided by the applicants’ in the claimed method and composition, has been provided by the applicants’, which would indicate that they had possession of the claimed genus of polypeptides and the encoding polynucleotides. As the claimed genera of polypeptides and encoding polynucleotides having widely variable structure and associated function, since minor changes in structure may result in changes affecting function and no additional information (species/variant/mutant) correlating structure with function has been provided. Furthermore, “Possession may not be shown by merely describing how to obtain possession of members of the claimed genus or how to identify their common structural features” (See University of Rochester, 358 F.3d at 927, 69 USPQ2d at 1895).
Therefore, one skilled in the art cannot reasonably conclude that applicant had possession of the claimed invention at the time the instant application was filed. Applicants are referred to the revised guidelines concerning compliance with the written description requirement of 35 U.S.C. 112(a) or 35 U.S.C. 112, first paragraph, published in the Official Gazette and also available at www.uspto.gov.
Enablement
II. Claims 34-48 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112, first paragraph, because the specification is enabling for the characterization of two species: polypeptides comprising the amino acid sequences of SEQ ID NO: 1 and SEQ ID NO: 2 and capable of biodegrading, or oxidizing and/or depolymerizing a polyolefin-derived polymer, has been provided by the applicants’ in the claimed method of making, method of use and composition. However, specification does not reasonably provide enablement for a genus of polypeptides and encoding polynucleotides i.e., a method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, comprising contacting: any enzyme capable of biodegrading, or oxidizing and/or depolymerizing a polyolefin-derived polymer including variants, mutants and homologs…, said enzyme having an amino acid sequence identity of at least 75% with SEQ ID NO: 1… (as in claims 34-37, 41-42 and 46-47); an expression vector comprising encoding nucleotide sequence, host cell comprising said expression vector and a method of expressing said encoded enzyme (as in claims 42-44) and a kit/composition comprising said enzyme (as in claim 48); and said method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, further comprising any second enzyme of undefined activity which comprises an amino acid sequence having an amino acid sequence identity of at least 75% with SEQ ID NO: 2 including variants, mutants and homologs (as in claims 38-40; also see claims objections and 35 U.S.C. 112(b) rejection above for claim interpretation). The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands (858 F.2d 731, 8 USPQ 2nd 1400 (Fed. Cir. 1988)) as follows: (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claim(s).
Claims 34-48 are so broad as to encompass: a genus of polypeptides and encoding polynucleotides i.e., a method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, comprising contacting: any enzyme capable of biodegrading, or oxidizing and/or depolymerizing a polyolefin-derived polymer including variants, mutants and homologs…, said enzyme having an amino acid sequence identity of at least 75% with SEQ ID NO: 1… (as in claims 34-37, 41-42 and 46-47); an expression vector comprising encoding nucleotide sequence, host cell comprising said expression vector and a method of expressing said encoded enzyme (as in claims 42-44) and a kit/composition comprising said enzyme (as in claim 48); and said method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, further comprising any second enzyme of undefined activity which comprises an amino acid sequence having an amino acid sequence identity of at least 75% with SEQ ID NO: 2 including variants, mutants and homologs (as in claims 38-40; also see claims objections and 35 U.S.C. 112(b) rejection above for claim interpretation). The scope of the claims is not commensurate with the enablement provided by the disclosure with regard to the extremely large number of polypeptides and encoding polynucleotides broadly encompassed by the claims. Since the amino acid sequence of a protein encoded by a polynucleotide determines its structural and functional properties, predictability of which changes can be tolerated in a protein's amino acid sequence and obtain the desired activity requires a knowledge of and guidance with regard to which amino acids in the protein's sequence and the respective codons in its polynucleotide, if any, are tolerant of modification and which are conserved (i.e., expectedly intolerant to modification), and detailed knowledge of the ways in which the encoded proteins' structure relates to its function. However, in this case the disclosure is limited to the characterization of two species: polypeptides comprising the amino acid sequences of SEQ ID NO: 1 and SEQ ID NO: 2 and capable of biodegrading, or oxidizing and/or depolymerizing a polyolefin-derived polymer, has been provided by the applicants’ in the claimed method of making, method of use and composition. It would require undue experimentation of the skilled artisan to make and use the claimed genus polypeptides and the encoding polynucleotides i.e., a method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, comprising contacting: any enzyme capable of biodegrading, or oxidizing and/or depolymerizing a polyolefin-derived polymer including variants, mutants and homologs…, said enzyme having an amino acid sequence identity of at least 75% with SEQ ID NO: 1… (as in claims 34-37, 41-42 and 46-47); an expression vector comprising encoding nucleotide sequence, host cell comprising said expression vector and a method of expressing said encoded enzyme (as in claims 42-44) and a kit/composition comprising said enzyme (as in claim 48); and said method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, further comprising any second enzyme of undefined activity which comprises an amino acid sequence having an amino acid sequence identity of at least 75% with SEQ ID NO: 2 including variants, mutants and homologs (as in claims 38-40; also see claims objections and 35 U.S.C. 112(b) rejection above for claim interpretation). The specification provides no guidance with regard to the making of variants and mutants or with regard to other uses as claimed in the instant claims. In view of the great breadth of the claims, amount of experimentation required to make and use the claimed polypeptides, the lack of guidance, working examples, and unpredictability of the art in predicting function from a polypeptide primary structure (for example, see Whisstock et al., Prediction of protein function from protein sequence and structure. Q Rev Biophys. 2003, Aug. 36 (3): 307-340), the claimed invention would require undue experimentation. As such, the specification fails to teach one of ordinary skill how to use the full scope of the polypeptides and the encoding polynucleotides encompassed by these claims.
While enzyme isolation techniques, recombinant and mutagenesis techniques are known, and it is not routine in the art to screen for multiple substitutions or multiple modifications as encompassed by the instant claims, the specific amino acid positions within a protein's sequence where amino acid modifications can be made with a reasonable expectation of success in obtaining the desired activity/utility are limited in any protein and the result of such modifications is unpredictable. In addition, one skilled in the art would expect any tolerance to modification for a given protein to diminish with each further and additional modification, e.g. multiple substitutions.
The specification does not support the broad scope of the claims which encompass: genus of polypeptides and encoding polynucleotides i.e., a method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, comprising contacting: any enzyme capable of biodegrading, or oxidizing and/or depolymerizing a polyolefin-derived polymer including variants, mutants and homologs…, said enzyme having an amino acid sequence identity of at least 75% with SEQ ID NO: 1…; an expression vector comprising encoding nucleotide sequence, host cell comprising said expression vector and a method of expressing said encoded enzyme and a kit/composition comprising said enzyme; and said method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, further comprising any second enzyme of undefined activity which comprises an amino acid sequence having an amino acid sequence identity of at least 75% with SEQ ID NO: 2 including variants, mutants and homologs (also see claims objections and 35 U.S.C. 112(b) rejection above for claim interpretation), as claimed in claims 34-48, because the specification does not establish: (A) a rational and predictable scheme for identifying an enzyme exhibiting desired activity and comprising an amino acid sequence having at least 75% sequence identity to SEQ ID NO: 1 or SEQ ID NO: 2 … and encoding polynucleotides of undefined structure, having amino acid residue changes and with an expectation of obtaining the desired biological function; (B) defined core regions/motifs involved in the desired catalytic activity of encoded polypeptides; (C) the tertiary structure of the molecule and folding patterns that are essential for the desired activity and tolerance to modifications; and (D) the specification provides insufficient guidance as to which of the essentially infinite possible choices is likely to be successful.
Thus, applicants’ have not provided sufficient guidance to enable one of ordinary skill in the art to make and use the claimed invention in a manner reasonably correlated with the scope of the claims broadly including polypeptides and encoding polynucleotides with an enormous number of modifications. The scope of the claim must bear a reasonable correlation with the scope of enablement (In re Fisher, 166 USPQ 19 24 (CCPA 1975)). Without sufficient guidance, determination of polypeptides and encoding polynucleotides having the desired biological characteristics is unpredictable and the experimentation left to those skilled in the art is unnecessarily, and improperly, extensive and undue. See In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988).
III. Claims 43-44 and 48 “A host cell …” as interpreted is directed to the use of multicellular organisms including transgenic animals and plants for producing protein of interest and is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112, first paragraph, as failing to comply with the enablement requirement when given the broadest reasonable interpretation, because, while claims 43-44 and 48 are enabling for an isolated host cell transformed with the recombinant expression vector encoding polypeptide(s) of interest, does not reasonably provide enablement for any transgenic multi-cellular organisms or host cells within a multi-cellular organism that have been transformed with the synthetic nucleic acid/expression vector or any transgenic plant that have been transformed with the synthetic nucleic acid/expression vector and expressing the polypeptide of interest. 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 the claims.
Claims 43-44 and 48 are so broad as to encompass transgenic multi-cellular organisms and host cells transformed with specific nucleic acids, including cells in vitro culture as well as within any multi-cellular organism and transgenic plants. The enablement provided is not commensurate in scope with the claim due to the extremely large number of transgenic multicellular organisms encompassed by the claims which the specification fails to teach how to generate. While methods for transforming cells in vitro are well known in the art, methods for successfully transforming cells within complex multi-cellular organisms are not routine and are highly unpredictable. Furthermore, methods for producing a successfully transformed cell within the multi-cellular organism are unlikely to be applicable to transformation of other types of multi-cellular organism, as multi-cellular organisms vary widely. However, in this case the disclosure is limited to only isolated cells. Thus, applicant has not provided sufficient guidance to enable one of ordinary skill in the art to make and use the claimed invention in a manner reasonably correlated with the scope of the claims broadly including the use of host cells within a multi-cellular organism for the production of said polypeptides. The scope of claims must bear a reasonable correlation with the scope of enablement (In re Fisher, 166 USPQ 19 24 (CCPA)). Without sufficient guidance, expression of genes in a particular host cell and having the desired biological characteristics is unpredictable, the experimentation left to those skilled in the art is unnecessarily, and improperly, extensive and undue. See In re Wands 858 F. 2d 731, 8 USPQ 2nd 1400 (Fed. Cir., 1988). It is suggested that the applicant limit the claim to “An isolated host cell …”.
Although the claims are examined in the light of the specification, specification cannot be read into the claims, i.e., the limitations of the specification cannot be read into the claims (see MPEP 2111 R-5).
415 F.3d at 1316, 75 USPQ2d at 1329. See also In re Hyatt, 211 F.3d 1367, 1372,54 USPQ2d 1664, 1667 (Fed. Cir. 2000). Applicant always has the opportunity to amend the claims during prosecution, and broad interpretation by the examiner reduces the possibility that the claim, once issued, will be interpreted more broadly than is justified. In re Prater, 415 F.2d 1393, 1404-05, 162 USPQ 541, 550-51 (CCPA 1969) (Claim 9 was directed to a process of analyzing data generated by mass spectrographic analysis of a gas. The process comprised selecting the data to be analyzed by subjecting the data to a mathematical manipulation. The examiner made rejections under 35 U.S.C. 101 and 102. In the 35 U.S.C. 102 rejection, the examiner explained that the claim was anticipated by a mental process augmented by pencil and paper markings. The court agreed that the claim was not limited to using a machine to carry out the process since the claim did not explicitly set forth the machine. The court explained that “reading a claim in light of the specification, to thereby interpret limitations explicitly recited in the claim, is a quite different thing from reading limitations of the specification into a claim,’ to thereby narrow the scope of the claim by implicitly adding disclosed limitations which have no express basis in the claim.” The court found that applicant was advocating the latter, i.e., the impermissible importation of subject matter from the specification into the claim.). See also In re Morris, 127 F.3d 1048, 1054-55, 44 USPQ2d 1023, 1027-28 (Fed. Cir. 1997) (The court held that the PTO is not required, in the course of prosecution, to interpret claims in applications in the same manner as a court would interpret claims in an infringement suit. Rather, the “PTO applies to verbiage of the proposed claims the broadest reasonable meaning of the words in their ordinary usage as they would be understood by one of ordinary skill in the art, taking into account whatever enlightenment by way of definitions or otherwise that may be afforded by the written description contained in applicant’s specification.”). The broadest reasonable interpretation of the claims must also be consistent with the interpretation that those skilled in the art would reach.
Claim Rejections: 35 USC § 103
The following is a quotation of 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims under 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of 35 U.S.C. 103(c) and potential 35 U.S.C. 102(e), (f) or (g) prior art under 35 U.S.C. 103(a).
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 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.
Claims 34-48 are rejected under 35 U.S.C. 103(a) as being unpatentable over (i) Bombelli et al., (Current Biol., 2017, Vol. 27, pages R283-R293, in IDS) and further in view of Memmel1 et al., (Insect Biochem. Mol. Biol., 1992, Vol. 22: 333-342, in IDS), Memmel2 et al., (Insect Biochem. Mol. Biol., 1994, Vol. 24: 133-144, in IDS), NCBI Reference Sequence: XP_026756396.1 disclosing arylphorin subunit alpha-like obtained from Galleria mellonella and having 100.0% sequence identity to SEQ ID NO: 1 of the instant invention, and NCBI Reference Sequence: XP_026756459.1 disclosing an acidic juvenile hormone-suppressible protein 2/Hemocyanin/hexamerin gene obtained from Galleria mellonella and having 100% sequence identity to SEQ ID NO: 2 of the instant invention (see provided sequence alignments).
Claims 34-48, as interpreted encompass a genus of polypeptides and encoding polynucleotides i.e., a method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, comprising contacting: any enzyme capable of biodegrading, or oxidizing and/or depolymerizing a polyolefin-derived polymer including variants, mutants and homologs…, said enzyme having an amino acid sequence identity of at least 75% with SEQ ID NO: 1… (as in claims 34-37, 41-42 and 46-47); an expression vector comprising encoding nucleotide sequence, host cell comprising said expression vector and a method of expressing said encoded enzyme (as in claims 42-44) and a kit/composition comprising said enzyme (as in claim 48); and said method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, further comprising any second enzyme of undefined activity which comprises an amino acid sequence having an amino acid sequence identity of at least 75% with SEQ ID NO: 2 including variants, mutants and homologs (as in claims 38-40; also see claims objections and 35 U.S.C. 112(b) rejection above for claim interpretation).
Regarding claims 34-48, the reference of Bombelli et al., (Current Biol., 2017, Vol. 27, pages R283-R293, in IDS) discloses the degradation of polyethylene (PE) when in direct contact by Galleria mellonella larvae at room temperature and suggest said breakdown of polyethylene (PE) is due to enzymatic activities and potential biotechnological applications (see Fig. 1 page R292; and pages R292 to R296; and entire document); examiner also notes that enzymes of the instant application comprising the amino acid sequences of SEQ ID NO: 1 and SEQ ID NO: 2 of the application have been isolated from Galleria mellonella larvae (page 7, lines 15-21; Examples, pages 22-33 of specification) and hence, cells of the larvae naturally comprise the polypeptides and the encoding nucleotide sequences of said enzymes of the instant application.
Memmel1 et al., (Insect Biochem. Mol. Biol., 1992, Vol. 22: 333-342, in IDS) disclose a polypeptide, encoding polynucleotide annotated as arylphorin gene obtained from Galleria mellonella and methods to clone and express the reference polypeptide, said reference polypeptide having 81.7% sequence identity to SEQ ID NO: 1 of the instant invention (see provided sequence alignment), and NCBI Reference Sequence: XP_026756396.1 discloses arylphorin subunit alpha-like obtained from Galleria mellonella and having 100.0% sequence identity to SEQ ID NO: 1 of the instant invention (see provided sequence alignment), and thus a skilled artisan is provided teaching, suggestion and motivation to clone and express the NCBI Reference Sequence: XP_026756396.1 disclosing arylphorin subunit alpha-like obtained from Galleria mellonella and having 100.0% sequence identity to SEQ ID NO: 1 of the instant invention based on the teachings of Bombelli et al., and Memmel1 et al.
Similarly, Memmel2 et al., (Insect Biochem. Mol. Biol., 1994, Vol. 24: 133-144, in IDS), disclose a polypeptide, encoding polynucleotide annotated as hexamerin gene obtained from Galleria mellonella and methods to clone and express the reference polypeptide, said reference polypeptide having 95.5% sequence identity to SEQ ID NO: 2 of the instant invention (see provided sequence alignment); applicants’ are directed to Abstract; Materials & Methods; Results; and entire document of Memmel2 et al., and NCBI Reference Sequence: XP_026756459.1 discloses an acidic juvenile hormone-suppressible protein 2/Hemocyanin/hexamerin gene obtained from Galleria mellonella and having 100% sequence identity to SEQ ID NO: 2 of the instant invention (see provided sequence alignment) and thus a skilled artisan is provided teaching, suggestion and motivation to clone and express the NCBI Reference Sequence: Sequence: XP_026756459.1 disclosing an acidic juvenile hormone-suppressible protein 2/Hemocyanin/hexamerin gene obtained from Galleria mellonella and having 100% sequence identity to SEQ ID NO: 2 of the instant invention based on the teachings of Bombelli et al., and Memmel2 et al., and it would be obvious for the skilled person to isolate the degradation products of the polyolefin-derived polymer (PE) after contacting the polymer with the host cell (larvae) or composition (worm homogenate) comprising the necessary enzymes and this activity is expected to be an inherent property of the structurally identical proteins (i.e., identical with SEQ ID NO: 1 and SEQ ID NO: 2 as disclosed by the prior art). It is routine for the skilled person to clone a known gene, i.e., to express the encoding polynucleotides in a host cell by means of an expression vector and as suggested in the teachings Bombelli et al., Memmel1 et al., and Memmel2 et al.
Hence, using the indications of Bombelli et al., Memmel1 et al., and Memmel2 et al., as a reference, it would have been easy for a person skilled in the art to use the polypeptides and the encoding DNA of NCBI Reference Sequence: XP_026756396.1 disclosing arylphorin subunit alpha-like obtained from Galleria mellonella and having 100.0% sequence identity to SEQ ID NO: 1 of the instant invention, and NCBI Reference Sequence: XP_026756459.1 disclosing an acidic juvenile hormone-suppressible protein 2/Hemocyanin/hexamerin gene obtained from Galleria mellonella and having 100% sequence identity to SEQ ID NO: 2 of the instant invention (see provided sequence alignments) to clone into an expression vector, transform host cells of interest and use the generated transformant to produce the polypeptides of interest and in a method of use for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer. One of ordinary skill in the art would have a reasonable expectation of success, since polypeptides having the biochemical properties of biodegrading a polyolefin, method of making and using said polypeptides are well known in the art (Bombelli et al., Memmel1 et al., and Memmel2 et al.,).
Therefore, claims 34-48 are rejected under 35 U.S.C. 103(a) as being unpatentable over (i) Bombelli et al., (Current Biol., 2017, Vol. 27, pages R283-R293, in IDS) and further in view of Memmel1 et al., (Insect Biochem. Mol. Biol., 1992, Vol. 22: 333-342, in IDS), Memmel2 et al., (Insect Biochem. Mol. Biol., 1994, Vol. 24: 133-144, in IDS), NCBI Reference Sequence: XP_026756396.1 disclosing arylphorin subunit alpha-like obtained from Galleria mellonella and having 100.0% sequence identity to SEQ ID NO: 1 of the instant invention, and NCBI Reference Sequence: XP_026756459.1 disclosing an acidic juvenile hormone-suppressible protein 2/Hemocyanin/hexamerin gene obtained from Galleria mellonella and having 100% sequence identity to SEQ ID NO: 2 of the instant invention (see provided sequence alignments).
Examiner also finds support in the following sections of MPEP.
2112 [R-3] Requirements of Rejection Based on Inherency; Burden of Proof
The express, implicit, and inherent disclosures of a prior art reference may be relied upon in the rejection of claims under 35 U.S.C.102 or 103. “The inherent teaching of a prior art reference, a question of fact, arises both in the context of anticipation and obviousness.” In re Napier, 55 F.3d 610, 613, 34 USPQ2d 1782, 1784 (Fed. Cir.1995) (affirmed a 35 U.S.C. 103 rejection based in part on inherent disclosure in one of the references). See also In re Grasselli, 713 F.2d 731, 739, 218 USPQ 769, 775 (Fed. Cir. 1983).
A REJECTION UNDER 35 U.S.C. 102/103 CAN BE MADE WHEN THE PRIOR ART PRODUCT SEEMS TO BE IDENTICAL EXCEPT THAT THE PRIOR ART IS SILENT AS TO AN INHERENT CHARACTERISTIC
Where applicant claims a composition in terms of a function, property or characteristic and the composition of the prior art is the same as that of the claim but the function is not explicitly disclosed by the reference, the examiner may make a rejection under both 35 U.S.C.102 and 103, expressed as a 102/103 rejection. “There is nothing inconsistent in concurrent rejections for obviousness under 35 U.S.C.103 and for anticipation under 35 U.S.C. 102.” In re Best, 562 F.2d 1252, 1255 n.4, 195 USPQ 430, 433 n.4 (CCPA 1977). This same rationale should also apply to product, apparatus, and process claims claimed in terms of function, property or characteristic. Therefore, a 35 U.S.C.102/103 rejection is appropriate for these types of claims as well as for composition claims.
Double Patenting rejections
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory obviousness-type double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); and In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on a nonstatutory double patenting ground provided the conflicting application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement.
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
Claims 34-48 of the instant application are rejected under the judicially created doctrine of obviousness-type double patenting as being unpatentable over the following co-pending applications: (a) over claims 1-43 of 19/134,612(Bertocchini et al.,); and (b) over claims 1-43 of 19/134,658 (Bertocchini et al.,). An obviousness-type double patenting rejection is appropriate where the conflicting claims are not identical, but an examined application claim is not patentably distinct from the reference claim, because the examined claim is either anticipated by, or would have been obvious over reference claim. See, e.g., In re Berg, 140 F.3d 1428,46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir.1993); In re Longi 759 F.2d 887,225 USPQ 645 (Fed. Cir. 1985). Although the conflicting claims are not identical, they are not patentably distinct from each other.
The recited claims of the recited reference co-pending applications above also encompass a genus of polypeptides and encoding polynucleotides i.e., a method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, comprising contacting: any enzyme is capable of biodegrading, or oxidizing and/or depolymerizing a polyolefin-derived polymer including variants, mutants and homologs…, an expression vector comprising encoding nucleotide sequence, host cell comprising said expression vector and a method of expressing said encoded and a kit/composition comprising said enzyme; and said method for biodegrading a polyolefin-derived polymer, or a material comprising a polyolefin-derived polymer, further comprising any second enzyme of undefined activity including variants, mutants and homologs as claimed in claims 34-48 of the instant application, and falls entirely within the scope of co-pending claims in co-pending reference applications, as the reference co-pending applications polypeptides and the encoding reference polynucleotides have 75% sequence identities to SEQ ID NO: 1 and SEQ ID NO: 2 of the instant application (see provided sequence alignments).
This is a provisional obviousness-type double patenting rejection because the conflicting claims have not in fact been patented.
Miscellaneous
A cursory review of the sequence search shows many applications filed by the current assignee of the instant application (Consejo Superior…) which discloses the encoding polynucleotide and polypeptides of SEQ ID NOs: 1 and 2. Furthermore, said SEQ ID NOs: 1 or 2 correspond to different SEQ ID NOs designation in different applications. The examiner has made an earnest attempt at identifying double patenting issues in some of these applications as shown above. However, in view of the large number of applications already filed and the fact that new applications are being filed, the examiner hereby requests applicants’ collaboration in pointing out to the examiner those applications which could raise double patenting issues that the examiner has not been able to identify; specifically sequences with different SEQ ID NOs and having 75% sequence identity to SEQ ID NO: 1 or 2 of the instant application.
Allowable Subject Matter/Conclusion
None of the claims are allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GANAPATHIRAMA RAGHU whose telephone number is (571)272-4533. The examiner can normally be reached on M-F 8:30am-5pm EST.
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/GANAPATHIRAMA RAGHU/ Primary Examiner, Art Unit 1652
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