DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
Claims 1-3, 6, 10, 15-16, 19, 21, 24, 26, 30, 34, 40-41, 45-46, and 48 are currently pending.
Priority
The present application claims status as a 371 (National Stage) of PCT/IL2022/050792 filed on 07/21/2022. Acknowledgment is made of applicant’s claim for benefit under 35 U.S.C. 119(e) of Provisional application No. 63/224,462, filed on 07/22/2021. The present application and all claims are being examined with an effective filing date of 07/22/2021. In future actions, the effective filing date may change due to amendments or further review of priority documents.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see pg. 34). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Objections
Claims 3, 10, 16, 21 and 26 are objected to because of the following informalities:
Claim 3 recites “(i) having an activity at pH ranging from…” in line 2. Please amend the claim to recite “(i) having an activity at a pH ranging from…”.
Claim 3 recites “(iv) being stable at temperature ranging…” in line 4. Please amend the claim to recite “(iv) being stable at a temperature ranging…”.
Claim 10 is objected to for the recitation “wherein said stable is comprising or maintaining…” in line 2, which is awkward wording and lacks clear antecedent for “said stable” within claim 6 itself. It is suggested that the claim be amended to recite “wherein said stability is comprising or maintaining” or “wherein said stability comprises maintaining…”.
Claim 16 recites “comprising a nucleic acid sequence being codon optimized…” in lines 2 and 3, which sounds like a process rather than a state. It is suggested that the claim be amended to recite “comprising a codon optimized nucleic acid sequence…”.
Claim 21 recites “optionally wherein any one of (i) said cell being any one of: a unicellular organism, a cell of a multicellular organism, and a cell in a culture” in lines 1-2, which contains redundant wording and uses inconsistent style/language compared to the limitation recited in “(ii)”. It is suggested that the claim be amended to recite, for example, “said cell is a unicellular organism, a cell from a multicellular organism, or a cell in a culture”.
Claim 26 recites “wherein said composition being characterized by being capable preventing or reducing food spoilage, and optionally wherein any one of: said food spoilage is induced by or involves any one of a bacterium and biofilm produced by same, and said bacterium comprises Pseudomonas fluorescens” in lines 2-5, which contains redundant wording and awkward phrasing. It is suggested that the claim be amended to recite, for example, “wherein said composition is characterized by being capable of preventing or reducing food spoilage and optionally wherein or biofilm produced by same, wherein said bacterium comprises Pseudomonas fluorescens”.
Appropriate correction for all of the above is required.
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.
Claims 1-3, 6, 10, 15-16, 19, 21, 24, 26, 30, 34, 40-41, 45-46, and 48 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.
Claim 1 (and claim 2-3, 6, 10, 15-16, 19, 21, 24, 26, 30, 34, 40-41, 45-46, and 48 dependent therefrom) are indefinite due to the recitation of “at least 95% homology or identity thereto” because it is unclear if the terms “homology” and “identity” are meant to be interchangeable, or two distinct metrics. The specification does not clearly define or distinguish between sequence “homology” and sequence “identity”, or provide parameters for measuring homology. While “identity” is understood as sequence alignment percentage, “homology” can refer to evolutionary relatedness or functional similarity, rather than a quantifiable metric. For examination purposes, homology and identity are being interpreted as interchangeable, measured according to sequence alignment.
Claim 30 is indefinite for the recitation of “an article”. The term “article” is unclear because the specification provides only non‑limiting examples (medical devices, organic waste processing devices, fluidic devices, agricultural devices, packages, sealing articles, fuel containers, water and cooling system devices, and construction elements) without defining parameters or structural features that distinguish an “article” from other substrates or objects. A person of ordinary skill in the art would not understand the precise metes and bounds of what qualifies as an “article.” For examination purposes under the broadest reasonable interpretation, claim 30 is interpreted as any substrate or object capable of incorporating the polypeptide of claim 1.
Claims 34 and 40-41 are indefinite for the recitation of “organic based contaminant”. The phrase “organic-based contaminant” is unclear because the specification does not define what constitutes an “organic based contaminant” or provide parameters distinguishing it from other organic materials. While later claims specify “biofilm” and “P. fluorescens” as the organic based contaminant, claims 34, 40, and 41 do not, thereby leaving their scope indeterminate. For examination purposes under the broadest reasonable interpretation, claims 34, 40, and 41 are interpreted as reciting any organic material.
Claim 41 is further indefinite for the recitation of “said composition is susceptible to formation of said organic based contaminant”. The phrase “susceptible to formation” is unclear because the specification does not define the degree or conditions under which a composition is considered to be “susceptible,” nor does it provide measurable criteria (e.g., probability, time frame, conditions). For examination purposes under the broadest reasonable interpretation, claim 41 is interpreted as any composition capable of developing organic contaminants under any conditions.
Claim 46 recites the recitation of “said biofilm”. There is insufficient antecedent basis for this limitation in the claim.
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 1-3, 6, 10, 15-16, 19, 21, 24, 26, and 30 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
In view of the 2019 PEG (“The 2019 Revised Patent Subject Matter Eligibility Guidance” (2019 PEG) found at https://www.govinfo.gov/content/pkg/FR-2019-01-07/pdf/2018-28282.pdf ), based upon an analysis with respect to the claims as a whole, claims 1-3, 6, 10, 15-16, 19, 21, 24, 26, and 30 do not recite something significantly different than a judicial exception. The rationale for this determination is explained below:
Claims 1-3, 6, 10, 15-16, 19, 21, 24, 26, are directed to one of the four categories of patent eligible subject matter because ; however 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 (these claims are interpreted in light of the most recent Guidelines (See “Subject Matter Eligibility” found at https://www.uspto.gov/patent/laws-and-regulations/examination-policy/subject-matter-eligibility ; as well as Subject Matter Eligibility Examples: Life Sciences at https://www.uspto.gov/sites/default/files/documents/ieg-may-2016-ex.pdf )
These claims are analyzed for eligibility in accordance with their broadest reasonable interpretation. In view of the Subject Matter Eligibility Test for Products and Processes and the Steps cited below (See flowchart at pages 10-11 at https://www.uspto.gov/sites/default/files/documents/peg_oct_2019_update.pdf ), the claims are directed to an ineligible product as further detailed below.
It is noted, claim 1 is taken as representative of the composition‑type claims for purposes of the §101 analysis, because the other rejected claims recite the same natural polypeptide of claim 1 in different, but still purely compositional, contexts (e.g., compositions, cells, extracts, articles, and polynucleotides encoding the same protein).
In this case, claim 1 is directed to a composition of matter (Step 1) and recites a natural phenomenon/product of nature (in this case, the naturally occurring alcohol) that is directed to a judicial exception (in this case, a naturally occurring bacterial protein)(Step 2A).
Claim 1 recites “an isolated polypeptide comprising the amino acid sequence [full 280 aa sequence] (SEQ ID NO:3), or a functional analog having at least 95% homology or identity thereto”. As discussed below, the limitations of claim 1 read on a naturally occurring marine bacterial protein and its naturally occurring close variants.
The record shows that SEQ ID NO:1 (317 aa) is 100% identical to a “phosphoric esterase‑related protein” from a SAR202 cluster bacterium, as evidenced below and by MDP6453723 (NCBI database, Aug 2023, cited in PTO-892), which was recovered from marine metagenomic samples (e.g., Tara Oceans), and that SEQ ID NO:3 is an internal fragment of this same natural protein corresponding exactly to residues 22–301.
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The specification itself characterizes this marine “lactonase‑related protein” (moLRP) as a phosphotriesterase‑like lactonase (PLL) from marine metagenomes, aligns it structurally with the thermostable quorum‑quenching lactonase GKL from Geobacillus caldoxylosilyticus, and identifies conserved catalytic/metal‑binding residues typical of this natural enzyme family. The applicants further state that three nearly identical (>99% identity) moLRP‑like proteins were identified in Tara metagenome assemblies and that additional >99% identity hits were found in NCBI, all belonging to marine Chloroflexi (SAR202‑like) organisms. Applicant’s own disclosure, together with the sequence identity data, thus demonstrates that the claimed polypeptide sequence(s) correspond to naturally occurring bacterial enzymes present in SAR202/Chloroflexi marine bacteria, and that SEQ ID NO:3 is simply the internal catalytic domain of that same natural polypeptide. The optional “functional analog having at least 95% homology or identity thereto” language, as defined in the specification, further encompasses substantially identical, conservatively substituted variants that maintain essentially the same ester‑hydrolase / quorum‑quenching activity, which includes naturally occurring >99% identity moLRP‑like proteins identified in environmental metagenomic data. Accordingly, claim 1 reads upon a naturally occurring composition of matter (a marine bacterial lactonase protein and its naturally occurring close homologs) and thus recites a nature‑based product limitation that does not exhibit markedly different characteristics from its naturally occurring counterpart. The claim is therefore directed to a product of nature exception (Step 2A).
Claims 2-3 recite particular sequences (SEQ ID NO:1, which is the full‑length 317 aa SAR202 protein) and activity/stability ranges such as “having an activity at pH ranging from 7.5 to 9.5,” “being stable at temperature ranging from 1 to 85 °C,” and “being stable at a salinity ranging from 0 to 5 M”, which the specification itself attributes to the same marine PLL‑type lactonase moLRP that is naturally occurring in SAR202/Chloroflexi bacteria, as shown by the metagenomic and MAG analysis. These ranges therefore describe inherent properties of the same natural protein and its close natural homologs, not structural or functional modifications that make the claimed product markedly different from nature.
Claims 6 and 10 similarly recite that the activity is “at least 50% compared to an optimal activity control” and that “stable” comprises “maintaining at least 50% of the activity compared to optimal conditions,” which the examples show to be inherent properties of the moLRP/SAR202 enzyme under the disclosed assay conditions. These are natural characteristics of the enzyme and do not impart a markedly different characteristic.
Under its broadest reasonable interpretation, claim 15 encompasses any polynucleotide that encodes the naturally occurring polypeptide defined in claim 1, including the naturally occurring genomic or mRNA sequence from the SAR202 bacterium that encodes this enzyme. As described above, the specification expressly identifies the marine source organism (SAR202/Chloroflexi) and provides evidence from Tara metagenomes and MAG assemblies that such a gene naturally exists in marine microbial genomes. Claim 16 further recites that the polynucleotide of claim 15 comprises a nucleic acid sequence that is codon-optimized for expression in a cell. However, codon optimization involves substitution of synonymous codons without altering the amino acid sequence of the encoded polynucleotide, and therefore does not result in a polynucleotide that is markedly different from the naturally occurring gene, as it encodes the same naturally occurring protein and retains the same functional characteristics. Claim 19 recites an artificial nucleic acid molecule or vector comprising the polynucleotide of claim 15. Under its broadest reasonable interpretation, the recitation of a “vector” encompasses naturally occurring vectors such as plasmids. Thus, claims 15-16 and 19 read on a polynucleotide encoding the natural SAR202 protein, and a naturally occurring vector (e.g., plasmid) comprising said polynucleotide, and is therefore directed to a product of nature exception.
Claim 21 recites: “A cell comprising the isolated polypeptide of claim 1”. Under the broadest reasonable interpretation, this encompasses a native SAR202 bacterial cell that naturally comprises the SAR202 lactonase protein (i.e., SEQ ID NOs: 1 and 3) within the cell. The claim does not require a recombinant host cell, non‑natural expression system, engineered localization, or any structural or functional change to the cell beyond the presence of the natural protein. A natural cell containing its natural protein is a product of nature and does not exhibit markedly different characteristics from its natural counterpart.
Claim 24 recites: “An extract obtained or derived from the cell of claim 21”. Because claim 21 reads on native SAR202 cells, claim 24 encompasses crude or partially purified extracts obtained or derived from such natural cells that contain the same natural protein. Preparation of cell extracts does not, by itself, create markedly different characteristics when the extract contains the same set of naturally occurring cellular components in conventional relative proportions. Thus, claim 24 remains directed to a product of nature exception.
Claim 26 recites: “A composition comprising the isolated polypeptide of claim 1 and an acceptable carrier”. Under BRI, “acceptable carrier” includes conventional carriers such as water, buffer, or physiologically acceptable salts. The claim therefore reads on, for example, a composition consisting of the natural SAR202 lactonase protein dissolved in water. Such a simple admixture of a natural protein with a conventional carrier does not confer markedly different characteristics compared to the natural protein itself. Thus, the composition of claim 26 is still directed to a product of nature exception.
Claim 30 recites: “An article comprising the isolated polypeptide of claim 1”. Without definitively defining what constitutes an “article”, the specification describes “articles” broadly as including medical devices, organic waste processing devices, fluidic devices, agricultural devices, packages, sealing articles, fuel containers, water and cooling system devices, and construction elements. Under BRI, claim 30 reads on an article (e.g., a surface, device, or container) that merely contains the natural protein of claim 1 present on or within it. The claim does not require any non‑natural structural modification of the article or of the protein, any specific mode of immobilization, or any functional change to the article beyond mere presence of the natural enzyme. Such an article is simply a conventional substrate carrying a natural protein and is thus directed to a product of nature exception without markedly different characteristics.
Accordingly, claims 1-3, 6, 10, 15, 21, 24, 26, and 30 recite nature-based products (the natural marine lactonase protein, its naturally occurring variants, and natural genes, cells, extracts, and simple compositions or articles containing it) that do not exhibit markedly different characteristics from their naturally occurring counterparts and are thus directed to a product of nature / natural phenomenon judicial exception under Step 2A.
Further, in view of prong 2 of Step 2A, the claims do not recite additional elements that amount to significantly more than the judicial exception. The additional limitations in claims 2-3, 6, 10, 21, 24, 26, and 30 are either merely reciting natural properties of the same enzyme (e.g., pH, temperature, and salinity activity/stability ranges; ≥50% activity) that the specification identifies as intrinsic to the natural moLRP/SAR202 protein, or merely placing the natural protein in a conventional context (cells, extracts, compositions with carriers, or articles) without specifying any new structure, arrangement, or function beyond the presence of the natural enzyme. These limitations describe what the natural product is or where it is found, but do not impose any meaningful restriction on the use of the judicial exception or apply it in a manner that effects a transformation or improvement in another technology or technical field under the 2019 PEG.
As to Step 2B, the claims do not recite additional elements that amount to “significantly more” than the judicial exception. The additional limitations are recited at a high level of generality and reflect well‑understood, routine, and conventional uses of natural enzymes and nucleic acids, such as expressing natural proteins in cells, preparing cell extracts, dissolving proteins in carriers, and coating or incorporating proteins into articles, all of which are standard techniques in the art. Such conventional context does not provide an inventive concept sufficient to transform the nature‑based product into a patent‑eligible application.
As such, the added limitations and elements discussed above are merely nominal components of the claims and do not change the focus of the claims from the natural protein (and its natural variants and encoding genes) as a product of nature. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception, because the additional limitations are recited at a high level of generality and reflect only well‑understood, routine, conventional uses of natural products. This judicial exception is not integrated into a practical application because the claims are drawn simply to the natural compound itself, its natural nucleic acids and cells, and simple compositions or articles containing it.
Therefore, claims 1-3, 6, 10, 15-16, 19, 21, 24, 26, and 30 do not recite eligible subject matter under 35 U.S.C. 101 in view of the subject matter eligibility test for products and product‑type claims, and the claimed invention is directed to non‑statutory subject matter.
Claim Rejections - 35 USC § 112(a)
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 1-3, 6, 10, 15-16, 19, 21, 24, 26, 30, 34, 40-41, 45-46, and 48 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.
It is noted that the specification defines a “functional analog” as “any polypeptide analogous to the isolated polypeptide of the invention and characterized by having essentially the same activity as the isolated polypeptide of the invention”. The specification also defines “activity” as encompassing or referring to ester bond hydrolysis. Therefore, claims 1 and 2 have been broadly interpreted as encompassing a genus of polypeptides having at least 95% homology or identity to the amino acid sequences set forth in SEQ ID NO: 3 and SEQ ID NO: 1, respectively, wherein said polypeptides retain the same degree of ester hydrolysis as the polypeptides of SEQ ID NOs: 1 and 3.
MPEP 2163 I. states that to “satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention.
MPEP 2163. II.A.3.(a) states that “Possession may be shown in many ways. For example, possession may be shown by describing an actual reduction to practice of the claimed invention. Possession may also be shown by a clear depiction of the invention in detailed drawings or in structural chemical formulas which permit a person skilled in the art to clearly recognize that inventor had possession of the claimed invention. An adequate written description of the invention may be shown by any description of sufficient, relevant, identifying characteristics so long as a person skilled in the art would recognize that the inventor had possession of the claimed invention.
According to MPEP 2163.II.A.3.(a).ii), “Satisfactory disclosure of a ‘representative number’ depends on whether one of skill in the art would recognize that the applicant was in possession of the necessary common attributes or features possessed by the members of the genus in view of the species disclosed. 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…Instead, the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are ‘representative of the full variety or scope of the genus,’ or by the establishment of ‘a reasonable structure-function correlation.’"
In the instant case, SEQ ID NO:1 (moLRP) is disclosed, but no other sequences are provided that meet the 95% identity threshold and demonstrate the required “essentially the same activity” (ester bond hydrolysis/quorum quenching) as defined in the specification. The specification mentions three >99% identity natural homologs from Tara metagenomes and NCBI hits, but no specific sequences for these homologs are disclosed, nor is there data confirming they retain the claimed functional activity. While the specification identifies conserved catalytic/metal‑binding residues (His23, His25, His178, His266, Asp301, carbamylated Lys145) in moLRP aligned with GKL, these residues are necessary but not sufficient to ensure that all 95–100% identity variants retain “essentially the same activity.” The specification provides no guidance on which of the remaining residues can be substituted while preserving the full functional profile across the genus, nor does it disclose any representative working examples of analogs within the 95–100% range. The mere recitation that analogs are “substantially identical” sequences with “conservative substitutions” that “display the abilities as described herein” is insufficient to describe the claimed genus. One skilled in the art would not recognize that applicants were in possession of the full scope of polypeptides having at least 95% homology or identity to SEQ ID NO:3 (claim 1) or SEQ ID NO:1 (claim 2) with the required functional activity, given only one disclosed species (moLRP) and generic substitution language.
Given this lack of description of the representative species encompassed by the genus of the claims, the specification fails to sufficiently describe the claimed invention in such full, clear, concise, and exact terms that a skilled artisan would recognize that applicants were in possession of the full scope of the claimed invention.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NAGHMEH NINA MOAZZAMI whose telephone number is (703)756-4770. The examiner can normally be reached Monday-Friday, 9:00-5:00.
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/NAGHMEH NINA MOAZZAMI/Examiner, Art Unit 1652
/ROBERT B MONDESI/Supervisory Patent Examiner, Art Unit 1652