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 .
Claims Status
Claims 1, 3-6, 8, 10-11, 14, 16, 18-19, 22, 24-27, 29, 32 and 34 are pending.
Claims 1, 3-6, 8, 10-11, 14, 16, 18-19, 22 and 24 are withdrawn from examination as being part of non-elected groups.
Claims 25-27, 29, 32 and 34 are being examined.
All previous objections and rejections not set forth below are withdrawn due to claim amendments by the Applicant.
Claim Rejections - 35 USC § 112(b)
Claims 25-27, 29, 32 and 34 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. This is new rejection necessitated by the claim amendments.
It is not clear to the Examiner what the term “portion thereof” in the enriched RAM refer to in amended claim 25. The term “portion thereof” in claim 25 is not defined by the claim, the specification also does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
Claim 25 also recited “… more than 3 fold in absolute abundance…” It is not clear to the Examiner what is meant by “absolute abundance”, especially when it is in comparison to RAM obtained from the soil surrounding the roots of a wildtype plant. Any comparison would make it relative.
Claim 25 recites, “…butanediol fermentation genes…”. The Applicant does not define what qualifies a gene to be considered as “butanediol fermentation gene”.
There are at least two types of butanediols (1,4 butanediol and 2,3 butanediol) known in the art which are produced by microorganisms (Held et al., WO 2018/140936 Al; p.5, para 0018, line 2; p.9, para 0033, line 4). Microorganisms can have one or more polynucleotides encoding for the enzymes of the 1,4-BDO pathway comprises succinyl-CoA synthetase (sucC), CoA-dependent succinate semialdehyde dehydrogenase (sucD), 4-hydroxybutyrate dehydrogenase (4hbD), 4-hydroxybutyryl CoA transferase (cat2), aldehyde dehydrogenase (ald), and/or alcohol dehydrogenase (adh) (Held et al., p.27, para 00104, line 2-5). On the other hand, microorganisms can have one or more polynucleotides encoding for the enzymes of the 2,3-BDO pathway encoding for an acetolactate synthase (AlsS), alpha-acetolactate decarboxylase (budA), and/or acetoin reductase (Held et al., p.21, para 0085, line 1-4).
Moreover, there are many enzymes involved in the production of one of the butanediols, 2,3 butanediol, from various substrates including glucose and other metabolites as part of pyruvate metabolism, as shown below (Ng et al.; Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering, 2012, Microbial Cell Factories, 11:68; Fig. 1).
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Each of the enzymes directly involved and the enzymes involved in production of the cofactors (e.g, NADH and NADP+) are encoded by one or more genes. All these genes are involved in production/fermentation of the 2,3 butanediol.
It is not clear to the Examiner which genes encoding the enzymes involved in butanediol fermentation is referred to by the term “butanediol fermentation genes”.
The Applicant describes, “enriched fermentation capacity” (as recited in claim 32) arising due to enriched RAM “can comprise 0-5% over those normally present” (page 21, para 0060, line 1) indicating that even zero percentage increase/enrichment can be included in enriched RAM. It is also unclear what is meant by “enriched fermentation capacity”, given that the fermentation capacity can have no difference from the capacity ‘normally present’.
All the claims depending from claim 25 inherit the indefiniteness of claim 25.
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.
New Matter
Claims 25-27, 29, 32 and 34 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 claims contain 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. This is a NEW MATTER rejection.
Claim 25 recites “…more than 3 fold in absolute abundance…” (line 5).
The Applicant describes “abundance” (spec, p.20, para 0059, line 1-2; p.32, para 00117, line 6) and “relative abundance” (spec, para 0006, Fig. 6; p.42, para 00117, line 10). The Applicant does not define or describe the term “absolute abundance”.
However, the application as originally filed fails to support, explicitly, implicitly or inherently, butanediol fermentation genes in terms absolute abundance. The specification only discusses abundance and relative abundances, but not “absolute abundance”.
Scope of Enablement
Claims 25-27, 29, 32 and 34 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for two butanediol fermentation genes (acetolactate decarboxylase and butanediol dehydrogenase), does not reasonably provide enablement for all the butanediol fermentation genes. 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 use the invention commensurate in scope with these claims.
The applicant describes enriched fermentation capacity comprising butanediol fermentation (spec, p.3, para 0016, line 2-3; p.20, para 0058, line 1-6). The Applicant describes that the enriched fermentation capacity can be gauged as the abundance of the sum of fermentation genes (p.20, para 0059, line 1-2) and such fermentation genes include butanediol fermentation, such as acetolactate decarboxylase and butanediol dehydrogenase (spec, p.21, para 0059, line 2-3; p.43, Table 1). The Applicant does not define what qualifies a gene to become a “butanediol fermentation gene” (as described above for 112(b) rejection). Held et al. describes many genes whose products are directly associated with butanediol fermentation/production, as discussed above.
The Applicant also does not describe any butanediol fermentation gene other than acetolactate decarboxylase and butanediol dehydrogenase in the context of enriched RAM as claimed. The Applicant does not provide any guidance to enrich RAM by merely containing at least 50% more butanediol fermentation genes.
Current status of the art also does not provide any guidance to enrich RAM by merely containing at least 50% more butanediol fermentation genes.
Undue trial and error experimentations would be needed to identity if any gene encoding a polypeptide (other than acetolactate decarboxylase and butanediol dehydrogenase) associated with butanediol fermentation would enrich RAM of a transgenic plant.
Based on breadth of the claims, lack of any working example, lack of guidance in the instant description or in prior art, the specification at the time of the application filed would not have taught one skilled in the art how to make and use the full scope of the claimed invention without performing undue experiments.
Claim Rejections - 35 USC § 101
Claims 25-27, 29, 32 and 34 are 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. The claims are drawn to an agricultural composition comprising an enriched root associated microbiome (RAM) or a portion thereof, wherein the enriched RAM is obtained from a genetically engineered plant. These are product by process claims. Patentability of the product (i.e., “agricultural composition comprising an root associated microbiome (RAM) or a portion thereof”) does not depend on the process including use of genetically engineered plants grown over it, as claimed (i.e., “obtained from a genetically engineered plant”) but on the product itself.
The Applicant describes, “the enriched RAM can comprise one or more viable microorganisms, one or more proteins, one or more sugars, one or more volatile organic
compounds (VOCs), or any combination thereof. For example, the proteins, sugars, or VOCs can be released by the root of the plant, or by the microorganisms. Any microbiome (not necessarily enabled or produced by plants, genetically engineered or not) with enriched RAM would satisfy the claim limitations (spec, p.19, para 50). Thus, the enriched RAM can comprise just one single microorganism. Any microbiome (not necessarily enabled or produced by plants, genetically engineered or not) including a single microorganism as part of the enriched RAM would satisfy the claim limitations.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because all the viable microorganisms are also naturally occurring. Moreover, the Applicant does not define the term “a portion thereof” in the context of root associated microbiome (RAM) and also does not specify how far (distance wise) the term “root associated” imply from the root(s) of the plant. It is well-known in the art that soil microbiome is naturally enriched when specific type of plants (e.g., nitrogen-fixing naturally occurring legume plants) are grown over it and/or specific type of fungus (e.g., Saccharomyces cerevisiae), bacteria (e.g., Klebsiella oxytoca, Bacillus subtilis, and E. aerogenes), or other microorganisms live there. Claims 25-29, 32, and 34 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
The composition of independent claim 25 comprises an “enriched root associated microbiome or a portion thereof”. Root associated microbiomes (RAM) occur in nature. The instant claims recite “a portion thereof” of the enriched RAM. However, the terms “surrounding” (how far from the transgenic roots the surrounding implies) and “a portion thereof” are not defined in the specification. Claim 25 also recites that the enriched RAM “is obtained from a genetically engineered plant”. However, a RAM is not actually in a plant, but rather is in the soil surrounding the roots of plants. The Applicant does not show if naturally occurring soil associated with naturally occurring plants from different agroclimatic regions mainly with different soil pH would be having any difference in terms of abundance of butanediol fermentation genes including acetolactate decarboxylase and butanediol dehydrogenase, as described by the Applicant (spec, p.21, para 0059, line 2-3; p.43, Table 1).
It is known in the art that many naturally bacteria and fungus, for example- Enterobacter aerogenes, Klebsiella Oxytoca (soil borne rhizobacterium), Saccharomyces cerevisiae (Ng et al., Abstract; Fig. 1), Klebsiella pneumonia, Serratia, Bacillus polymyxa (Ng et al., p.1, right column, para 1, line 1-4), Bacillus amyloliquefaciens (Ng et al., p.2, left column, para 1, line 3) can produce butanediol.
Naturally occurring yeast (Saccharomyces cerevisiae) is found in almost all ecosystems including soil. Their population in soil ranges from a few to several thousand based on the soil ecosystem. Soil edaphic factors determine the abundance and diversity of yeasts. Sugar-rich plant residues, such as fruit debris, root exudates, forest soil, etc., support yeast growth (Devi et al., Potentials of Soil Yeasts for Plant Growth and Soil Health in Agriculture: A Review, 2025, J. Pure Appl. Microbiol., 19:1-18; Abstract, line 1-5). Soil yeasts are known to significantly influence the soil’s physical (macro and micro aggregates formation), soil chemical (pH, Soil Organic Carbon, Soil Labile Carbon, Soil Protein Index), and soil biological properties (Dehydrogenase activity, Microbial Biomass Carbon, Extracellular Polymeric Substances (EPS) production). Application of yeasts resulted in a yield increase in the range of 20-30% in crops like wheat and sugarbeet (Devi et al., abstract, line 11-15).
Naturally occurring Bacillus subtilis, which is abundant in healthy soils and the rhizosphere, is also known to contain all the genes needed and capable to produce 2,3-butanediol (Nicholson, WL, The Bacillus subtilis ydjL (bdhA) Gene Encodes Acetoin Reductase/2,3-Butanediol Dehydrogenase, 2008, Applied and Environmental Microbiology, 74:6832–6838; Abstract). Any naturally occurring soil or “a portion thereof” (with or without the transgenic plant) comprising at least 50% more of such microorganisms would have “greater than 50% in butanediol fermentation genes” enriched RAM and satisfy the claim limitations.
Further, the specification in [0034] teaches, “A “genetically engineered plant” can refer to a plant that has been genetically manipulated”, which includes “other forms of altering the amount, nature, or activity of nucleic acids in a plant, such as mutagenizing plant by exposing it to a mutagen such as UV light”. Therefore, a “genetically engineered plant” includes naturally-occurring mutated plants, as plants in nature are exposed to UV radiation in sunlight. An “enriched RAM” may also be the RAM surrounding the roots of such plants.
When a claim recites a nature-based product limitation, the markedly different characteristics analysis is used to evaluate the nature-based product limitation (MPEP 2106.04(b)(II)). Given it is unclear what is encompassed by the term “a portion thereof” and “surrounding” in the context of the invention, the claim encompasses RAM that occur in nature. As mentioned above, claim 25 does not require the RAM surrounding the roots of a genetically engineered plant to be any different in any specific way other than having at least 50% more butanediol fermentation genes from any source.
Further, the definition for “genetically engineered plant” in the specification encompasses naturally occurring plants mutagenized by UV in sunlight. Furthermore, the claim encompasses “a portion” of the enriched RAM. Neither the claims nor the specification place restrictions on this “portion”. Therefore, the “portion” encompasses any content including a specific microorganism with 50% more butanediol fermentation genes compared to another microorganism (not necessarily the same species) living around the roots of a non-transgenic plant. Such “portions” are not markedly different from the naturally-occurring microorganisms in naturally occurring RAM. And there are plenty of soil-borne microorganisms which do not have the ability to produce butanediol and do not have butanediol fermentation genes while there are so many other soil-borne microorganisms that have butanediol fermentation genes, as discussed above.
Claim 26 recites that the genetically-engineered plant overexpresses a type 1 H+-pyrophospatase. The claim encompasses any “portion” of an enriched RAM, which includes naturally occurring microorganims.
Claim 27 only limits the genetically engineered plant to being Arabidopsis. A RAM is not actually in a plant.
Claim 29 recites a Markush list of viable microorganisms comprised in the enriched RAM. Note, all of the Markush group members occur in nature, and constitute a “portion” of the enriched RAM.
Claim 32 depends from claim 29 and requires the viable microorganisms to comprise enriched fermentation capacity. As discussed above, there are plenty of soil-borne microorganisms which do not have the ability to produce butanediol and do not have butanediol fermentation genes while there are so many other soil-borne microorganisms that have “enriched (butanediol) fermentation capacity” while having the butanediol fermentation genes, as discussed above. Moreover, as discussed further in the rejection under 35 U.S.C. 112(b), the specification does not provide an unambiguous definition of “enriched fermentation capacity” that distinguishes from non-enriched fermentation capacity. For example, paragraph [0060] states, “For example, the enriched fermentation capacity can comprise 0-5% over those normally present,….”.
Claim 34 recites a Markush group of metabolites that the enriched RAM further comprises. However, this list also encompasses naturally-occurring substances (“at least one other plant nutrient”, at least).
The claims also do not recite any limitations that integrate the JEs into a practical application.
The claims recite, “The agricultural composition”. The specification in paragraph [0075] indicates that an agricultural composition “can refer to a composition that can improve the rate of growth or health of plants…and/or improving or change the environments where the plants grow”. The term “can” indicates that the composition does not necessarily improve the growth or health of plants or change the environment where they grow. Further, this is an intended use. The claims do not recite elements that add significantly more to the claims.
Thus, the claims are not directed to significantly more than the products of nature.
Response to Applicant’s arguments: Applicant’s argument has been fully considered but not found persuasive. The Applicant argues, “claim 25 as amended is drawn to an agricultural composition comprising an enriched root associated microbiome (RAM) or a portion thereof, wherein the enriched RAM is obtained from the soil surrounding the roots of a transgenic plant.” All the claims are product by process claims. Patentability of the product (i.e., “agricultural composition comprising an root associated microbiome (RAM) or a portion thereof”) does not depend on the process including use of genetically engineered plants grown over it, as claimed (i.e., “obtained from a genetically engineered plant”) but on the product itself. Any microbiome (not necessarily enabled or produced by plants, genetically engineered or not) with enriched RAM would satisfy the claim limitations, as discussed above.
Claim Rejections - 35 USC § 102(a)(1)
Claims 25-27, 29, 32 and 34 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kumar et al. (Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production, 2020, Journal of Advanced Research, 24:337–352), in evidence of Ng et al. (Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering, 2012, Microbial Cell Factories, 11:68) and Nicholson, WL (The Bacillus subtilis ydjL (bdhA) Gene Encodes Acetoin Reductase/2,3-Butanediol Dehydrogenase, 2008, Applied and Environmental Microbiology, 74:6832–6838).
Kumar et al. teaches targeted application of beneficial (reads on to “enriched”) plant microbiome including rhizosphere microbiome (which reads on to “root associated microbiome”) and their cocktails (which, cumulatively, reads on to “agricultural composition”) to counteract abiotic and biotic stresses in plants (abstract, line 4-5). Kumar et al. describes shaping rhizosphere microbiome of a susceptible host plant from a resistant plant which comprises specific type of microbial community with multiple potential benefits, and manipulation of susceptibility genes in crop plants for improving plant health (abstract, line 9-12). Kumar et al. also describes manipulating the pH of the rhizosphere by using genetically engineered or transgenic Arabidopsis plants (as recited in claims 25 and 27) overexpressing AVP1 H+ pyrophosphatase, which is a known type I pyrophosphatase1 (as recited in claim 26), producing different phenotypes including elevation of H+ -efflux from the roots of the plant, creates a more acidic environment in the rhizosphere which result in enhanced growth at lower pH, phosphate mineralization or plant mineral nutrition and exhibit enhanced resistance towards drought stress in AVP1 overexpressing Arabidopsis plants (page 344, left column, para 3, line 23-32). Kumar et al. also describes enriched RAM comprising different groups of bacteria (as recited in claim 29) including phosphate solubilizing bacteria (PSB), siderophore producing bacteria, and AMF increase accessibility of diverse plant nutrients such as iron, phosphorous, zinc, cooper, and cadmium (page 341, right column, para 4, line 18-21), as recited in claim 34. These rhizobacteria are also recognized as potential and commercially valuable biocontrol agents, like Bacillus, Streptomyces and Pseudomonads and produces antibiotic as well as antifungal compounds (page 341, right column, para 4, line 21-24). Kumar et al. describes RAM associated with different plants comprising various bacteria including Serratia spp. (p.342, left column, para 1, line 18), Enterobacter spp., and Klebsiella spp. (p.338, Table 1). At least few of the Enterobacter spp. (e.g., E. aerogenes), Klebsiella spp. (e.g., K. Oxytoca and K. pneumonia) and Serratia spp. (Ng et al., p.1, right column, para 1, line 1-4) besides several Bacillus spp. including Bacillus polymyxa (Ng et al., p.1, right column, para 1, line 1-4), Bacillus amyloliquefaciens (Ng et al., p.2, left column, para 1, line 3) and Bacillus subtilis (Nicholson, WL, Abstract) are known to produce butanediol, which implies that the bacteria contain all the genes needed to produce butanediol. Thus, any RAM enriched by at least 50% in such bacterial species, as described by Kumar et al., would be having greater than 50% in butanediol fermentation genes (as recited in claim 1) leading to enriched fermentation capacity, as recited in claim 32.
Response to Applicant’s arguments: Applicant’s arguments are fully considered but not found persuasive. The Applicant argues, “Kumar et al. does not teach an agricultural composition comprising a root associated microbiome or portion thereof with enriched butanediol fermentation capacity”.
The Examiner disagrees. Kumar et al. describes RAM associated with different plants comprising various bacteria including Serratia spp. (p.342, left column, para 1, line 18), Enterobacter spp., and Klebsiella spp. (p.338, Table 1). At least few of the Enterobacter spp. (e.g., E. aerogenes), Klebsiella spp. (e.g., K. Oxytoca and K. pneumonia), Serratia spp., several Bacillus spp. including Bacillus polymyxa, Bacillus amyloliquefaciens and Bacillus subtilis are known to produce butanediol, which implies that the bacteria contain all the genes needed to produce butanediol. Thus, any RAM enriched by at least 50% in any one of such bacterial species would be having greater than 50% in butanediol fermentation genes leading to enriched fermentation capacity,
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Communication
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Jay Chatterjee
Patent Examiner
Art Unit 1662
/Jay Chatterjee/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1661 & 1662
1 Pizzio et al. (Arabidopsis Type I Proton-Pumping Pyrophosphatase Expresses Strongly in Phloem, Where It Is Required for Pyrophosphate Metabolism and Photosynthate Partitioning, 2015, Plant Physiology, 167:541–1553) provides the evidence that AVP1 is a Type I pyrophosphatase (abstract, line 3-4).
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