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 .
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-5 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 purpose of the written description requirement is to ensure that the inventor had possession, at the time the invention was made, of the specific subject matter claimed. For a broad generic claim, the specification must provide adequate written description to identify the genus of the claim.
“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." Fiers, 984 F.2d at 1171, 25 USPQ2d 1601; In re Smythe, 480 F.2d 1376, 1383, 178 USPQ 279, 284985 (CCPA 1973) (“In other cases, particularly but not necessarily, chemical cases, where there is unpredictability in performance of certain species or subcombinations other than those specifically enumerated, one skilled in the art may be found not to have been placed in possession of a genus.”). Regents of the University of California v. Eli Lilly & Co., 119, F.3d 1559, 1568, 43 USPQ2d 1398, 1405 (Fed. Cir. 1997).
“The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice . . ., reduction to drawings . . ., or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus.” MPEP 2163(II)(3)(a).
Furthermore, 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. The disclosure of only one species encompassed within a genus adequately describes a claim directed to that genus only if the disclosure ‘indicates that the patentee has invented species sufficient to constitute the gen[us].’ See Enzo Biochem, 323 F.3d at 966, 63 USPQ2d at 1615; Noelle v. Lederman, 355 F.3d 1343, 1350, 69 USPQ2d 1508, 1514 (Fed. Cir. 2004) (Fed. Cir. 2004) (‘[A] patentee of a biotechnological invention cannot necessarily claim a genus after only describing a limited number of species because there may be unpredictability in the results obtained from species other than those specifically enumerated.’). ‘A patentee will not be deemed to have invented species sufficient to constitute the genus by virtue of having disclosed a single species when … the evidence indicates ordinary artisans could not predict the operability in the invention of any species other than the one disclosed.’ In re Curtis, 354 F.3d 1347, 1358, 69 USPQ2d 1274, 1282 (Fed. Cir. 2004).” MPEP 2163(II)(3)(a).
The claims recite a genus of lactic acid bacteria producing plasmalogen under aerobic conditions, as defined by the specification. The specification, para. [0021], provides: “Aerobic conditions refer to conditions in which oxygen is contained in the atmosphere. Aerobic conditions also include microaerobic conditions. In particular, culturing under aerobic conditions refers to culturing that is performed without the use of reagents and equipment to be used for culturing microorganisms under anaerobic conditions.”
The specification, para. [0007], sets forth that “no plasmalogen synthesis has been confirmed in facultative anaerobes and aerobic bacteria.” Enterococcus faecalis is a well-known facultative anaerobe. See Krishnan et al. (The MIC and MBC of Silver Nanoparticles against Enterococcus faecalis - A Facultative Anaerobe, J. Nanomedicine Nanotechnology 6, 2015, 3). The specification, para. [0007], states “plasmalogen synthesis by some obligate anaerobes such as Enterococcus faecalis, and the specification states “examples of the lactic acid bacteria for plasmalogen synthesis include Streptococcus equinus, Streptococcus mutans, Lactobacillus coryniformis, and Enterococcus faecalis.” Specification, para. [0024]. The specification appears to incorrectly label E. faecalis as an obligate anaerobe when it is a facultative anaerobe. Regardless, the specification correctly identifies E. faecalis as a lactic acid bacterium.
In view of the above, E. faecalis is the only apparent lactic acid bacterium characterized in the prior art to produce plasmalogen.
“In other cases, particularly but not necessarily, chemical cases, where there is unpredictability in performance of certain species or subcombinations other than those specifically enumerated, one skilled in the art may be found not to have been placed in possession of a genus.” “The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice . . ., reduction to drawings . . ., or by disclosure of relevant, identifying characteristics.”
In addition to E. faecalis discussed above, the specification identifies Lactobacillus coriniformis (JCM1166), Streptococcus mutans (JCM5705) and Streptococcus equinus (JCM7879) as producing plasmalogen. The specification asserts that production of plasmalogen by other lactic acid bacteria is not known in the prior art. As such, it is unpredictable regarding which additional lactic acid bacteria are functional for producing plasmalogen other than the specifically enumerated species. Stated in other words, lactic acid bacteria is a large genus of bacteria that is not adequately represented by a total of four species even when limited to three specific families as recited in claim 2. The disclosure of four specific species of lactic acid bacteria in the specification does not allow for the identification of other undisclosed lactic acid bacteria having ability to produce plasmalogen particular in view of an assertion in the specification that production of plasmalogens is an uncommon property in lactic acid bacteria. “The inventors of the present disclosure have screened various lactic acid bacteria, discovered that specific lactic acid bacteria synthesize plasmalogens under aerobic conditions, and thus completed the present disclosure.” Specification, para. [0012]. That is, the specification discloses that additional lactic acid bacteria synthesizing plasmalogens can only be identified by random screening for the same and there is no ready way to predict additional member species of the recited genus of lactic acid bacteria producing plasmalogen such that the specification does not disclose either a representative number of species of such genus nor a disclosure of relevant, identifying characteristics that allows for reasonable identification of other unenumerated members of such genus. For this reasons, there is inadequate written description of a genus of lactic acid bacteria producing plasmalogen as recited in claim 1 and incorporated in claims 2-5.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 3 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 3 depends from claim 1. Claim 1 requires a lactic acid bacterium. A bacterium is a living cell that inherently requires certain structures including a cell membrane, ribosomes and a chromosome. Claim 3 recites a composition comprising the cell of claim 1 or “a processed product thereof.” As such, a complete embodiment of claim 3 is a product processed from the bacterium of claim 1 that does not require the structure of a complete bacterial cell as required by claims 1.
That is, a complete embodiment of claim 3 would be a composition containing a purified plasmalogen in the absence of any bacterial cell; however, the same composition does not meet the limitations the limitations of claim 1 since no lactic acid bacterium is present in the composition. As such, claim 3 does not include all of the limitations of claim 1 from which claim 3 depends wherein the requirement for a lactic acid bacterium recited in claim 1 is missing and not required by claim 3.
It is noted that embodiments of claim 3 can be produced with the use of a lactic acid bacterium of claim 1. "[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process." MPEP 2113(I). A chemically-identical plasmalogen (e.g. processed product) obtained from the lactic acid bacterium of claim 1 can also be obtained from organisms that are not lactic acid bacteria or be chemically synthesized without the involvement of any cell/organism.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1-3 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Jackson et al. (Plasmalogen Biosynthesis by Anaerobic Bacteria, ACS Chem. Biol. 16, Dec. 2020, 6-13).
Jackson discloses the following:
Previous reports suggested that plasmalogens are not present in facultative anaerobic bacteria; however, we identified the pls operon as a single gene in several facultative anaerobes, including Enterococcus faecalis, a common gut microbe that can also cause opportunistic infections (see Figure 4A). The E. faecalis gene EF1327 encodes all activation and reduction/ dehydration domains as a single polypeptide (PlsA), with overall sequence identity of 48% when compared to PlsAR from C. perfringens. The relatively high protein sequence identity between PlsA (E. faecalis) and PlsAR (C. perfringens) suggested that E. faecalis may have the biosynthetic capacity to produce plasmalogens. We cultured E. faecalis under anaerobic and aerobic conditions in liquid culture and detected plasmalogen production under anaerobic but not aerobic conditions, as determined by Schiff staining and GC-MS analysis of plasmalogen-derived DMAs (see Figures 4B and 4C, as well as Figure S9). Jackson, page 11, left col.
“We also cultured E. faecalis under aerobic and anaerobic conditions on agar; we observed robust purple staining of anaerobically grown colonies and, notably, a more complex staining pattern for aerobically grown colonies (Figure 4D). For aerobically grown colonies, it appeared that only the colony interior was stained purple, while the exterior remained unstained and white. This argues that plasmalogen production in aerobically grown colonies is spatially restricted to the colony interior, where oxygen is limited.” Jackson, page 11, left col.
Enterococcus faecalis is a member of the Enterococcaceae family and the order Lactobacillales and a lactic acid bacterium as defined by the specification. “Specifically, examples of the lactic acid bacteria for plasmalogen synthesis include Streptococcus equinus, Streptococcus mutans, Lactobacillus coryniformis, and Enterococcus faecalis.” Specification, para. [0024].
The specification, para. [0021], provides: “Aerobic conditions refer to conditions in which oxygen is contained in the atmosphere. Aerobic conditions also include microaerobic conditions. In particular, culturing under aerobic conditions refers to culturing that is performed without the use of reagents and equipment to be used for culturing microorganisms under anaerobic conditions.”
Culturing of E. faecalis under aerobic conditions on agar wherein only the interior was stained purple such that plasmalogen production in aerobically grown colonies is spatially restricted to the colony interior meets the description of the specification of “culturing that is performed without the use of reagents and equipment to be used for culturing microorganisms under anaerobic conditions” (i.e. oxygen is generally not excluded from the atmosphere and/or environment of the culture) such that Jackson describes E. faecalis producing plasmalogen under an aerobic culture condition and a step of culturing E. faecalis and producing plasmalogen.
The specification does not discuss any difference in a pattern, quality or degree of plasmalogen production required by embodiment cells of claim 1 to be present between aerobic and anaerobic conditions. As such, the broadest reasonable interpretation of the claims does not require an increase of plasmalogen production under aerobic as compared to anaerobic conditions. Rather, the claims only require the production of some amount of plasmalogen through “culturing that is performed without the use of reagents and equipment to be used for culturing microorganisms under anaerobic conditions,” which is disclosed by Jackson. It is further observed that the “static culture” described in para. [0035] of the specification would be understood by an ordinarily skilled artisan at time of filing of having a gradient of oxygen concentration with greater concentration near the interface of the liquid culture and atmosphere and less oxygen at a distance from such interface similar to the interior and exterior of E. faecalis colonies as described by Jackson. As such, the disclosure of Jackson is consistent with the disclosure of the specification regarding potential effects of oxygen on plasmalogen production by lactic acid bacteria.
For these reasons, Jackson anticipates at least the features of claims 1-3. Aerobic grown E. faecalis on agar producing plasmalogen in interior of colonies is a composition as recited in claim 3.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1-5 is/are rejected under 35 U.S.C. 103 as being unpatentable over Jackson et al. (Plasmalogen Biosynthesis by Anaerobic Bacteria, ACS Chem. Biol. 16, Dec. 2020, 6-13).
The rejections of claims 1-3 as anticipated by Jackson under 35 USC 102(a)(1) set forth above are incorporated herein by reference.
Regarding claims 4 and 5, Jackson does not directly describe “obtaining a plasmalogen from a cell of the lactic acid bacterium,” which is understood as an additional step of at least partially isolating the plasmalogen in addition to producing plasmalogen in the separate “culturing” step.
Jackson, page 11, right col., states the following:
Pellets from 5 mL of liquid culture were stained with Schiff
Reagent to verify the plasmalogen-deficient phenotype and both
mutants were verified as C. perfringens by 16S rRNA sequencing.
Furthermore, cell pellets from 50 mL cultures were extracted with
chloroform:methanol (1:1) to yield crude lipid extracts, which were
sent to Microbial ID, Inc. for GC-MS analysis of lipid-derived fatty
acid methyl esters (FAMEs) and plasmalogen-derived dimethyl
acetals (DMAs) (see Figure S2).
Jackson does not state isolating lipids from E. faecalis, whether grown on agar under anaerobic or aerobic conditions. As shown in Fig. S2 of Jackson, there is an interest in determining the specific chemical make-up of plasmalogen lipids produced by cells. As such, at the time of filing an ordinarily skilled artisan would have been motivated to perform a chloroform:methanol extraction of lipids from E. faecalis cells as cultured by Jackson (under both or either of aerobic and anaerobic conditions) in order to determine the chemical composition of the plasmalogen lipids produced, which Jackson teaches that it is desirable and advantageous to determine the chemical composition of plasmalogen lipids produced by bacteria. Production of a crude lipid extract by chloroform:methanol extraction from cells is within the broadest reasonable interpretation of “obtaining a plasmalogen from a cell.” As discussed above, Jackson teaches culturing a lactic acid bacterium (E. faecalis) under aerobic conditions to produce plasmalogen.
Regarding claim 5, the culturing or growth of colonies on agar (a solid medium) as taught by Jackson is within the broadest reasonable interpretation of “statically cultured” wherein stirring or agitation of the otherwise solid media does not occur.
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 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon without significantly more. The claim(s) recite(s) a natural phenomenon being naturally-occurring bacterial cells. This judicial exception is not integrated into a practical application because the claims recite no limitations that can be considered to be a practical application. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims do not recite any limitations other than mixtures of natural products.
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. Step 2A into two prongs as set forth in MPEP 2106.04(II)(A).
“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 recites a "product of nature" exception, and requires further analysis in Step 2A Prong Two to “determine whether the claim as a whole integrates the exception into a practical application.” 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 is part of Step 2A Prong One, because the courts use this analysis to identify product of nature exceptions.” MPEP 2106.04(c). “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.” MPEP 2106.04(c)(II).
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.” MPEP 2106.04(c)(I).
Claims 1-3 (here “the claims”) are directed towards a composition of matter such that step 1 is yes. The specification identifies Lactobacillus coriniformis (JCM1166), Streptococcus mutans (JCM5705) and Streptococcus equinus (JCM7879) as producing plasmalogen as embodiments of claims 1-2. Further, as discussed above, Jackson (Plasmalogen Biosynthesis by Anaerobic Bacteria, ACS Chem. Biol. 16, Dec. 2020, 6-13) disclose an E. faecalis strain that is an embodiment of claims 1 and 2. All of these lactic acid bacterial cells are understood to be naturally-occurring microorganisms that are not modified by the hand of man. For example, “we identified the pls operon as a single gene in several facultative anaerobes, including Enterococcus faecalis, a common gut microbe that can also cause opportunistic infections,” which is a direct indication that at least E. faecium strains as taught by Jackson to be embodiments of claims 1 and 2 are understood to be products of nature. Jackson, page 11, left col. Further, the Lactobacillus coriniformis (JCM1166), Streptococcus mutans (JCM5705) and Streptococcus equinus (JCM7879) strains disclosed by the specification as embodiments of claims 1 and 2 are understood to be products of nature.
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.” MPEP 2106.04(c)(I). Here, a lactic acid bacterium of Streptococcaceae, Lactobacillaceae or Enterococcaceae synthesizing a plasmalogen under an aerobic condition are naturally occurring such that 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. Such that step 2A, prong one, is satisfied against patent eligibility for claims 1-2. For claim 3, claims 3 recites the lactic acid bacteria of claim 1 in a generic composition, such that an embodiment of claim 3, for example, is the bacterium of claim 1 combined with water wherein water is also a product of nature. There is no evidence of record that the inclusion of the naturally-occurring lactic acid bacteria discussed above in a generic composition results in any markedly different characteristic such that the step 2A, prong one, is satisfied against patent eligibility for claim 3.
Regarding step 2A, prong 2, the claims recite a lactic acid bacterium and generic compositions containing the same that do not amount to recitation of any additional claim features that integrate the product of nature exception into a practical application.
Regarding step 2B, “Step 2B asks: Does the claim recite additional elements that amount to significantly more than the judicial exception”? MPEP 2106.05(II). Here, claims 1 and 2 recite no additional elements other than the product of nature exception and claim 3 recites a generic composition, that does not amount to significantly more than the judicial exception.
For these reasons, the claims do not recite eligible subject matter.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to TODD M EPSTEIN whose telephone number is (571)272-5141. The examiner can normally be reached Mon-Fri 9:00a-5:30p.
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/TODD M EPSTEIN/Primary Examiner, Art Unit 1652
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