Notice of Pre-AIA or AIA Status
Objections and rejections are withdrawn unless restated below.
Claim 18 remains withdrawn.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Interpretation
Any fermenter or vessel discussed below for culturing a microorganism is a reactor as recited in the claims.
Clostridium thermocellum and Hungateiclostridium thermocellum are the same organism. See Ha-Tran (Utilization of Monosaccharides by Hungateiclostridium thermocellum ATCC 27405 through Adaptive Evolution, Microorganisms 9, 2021, 1445).
Claim Objections
Claim 15 is objected to because of the following informalities:
Claim 15, line 1, recites “A process for the biological production of hydrogen and/or methane.” The recited biological production is considered to have antecedent basis in the method defined by claim 15. Nevertheless, the underlined article “the” is extraneous and should be removed.
Appropriate correction is required.
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 15-17, 19-24 and 26-29 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).
MPEP § 2163 further states that if a biomolecule is described only by a functional characteristic, without any disclosed correlation between function and structure of the biomolecule, it is "not sufficient characteristic for written description purposes, even when accompanied by a method of obtaining the claimed biomolecule.”
“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 “process for the biological production of hydrogen . . . by biological absorption of carbon dioxide.” The term “biological adsorption” does not appear in the as-filed claims or specification. “During patent examination, the pending claims must be "given their broadest reasonable interpretation consistent with the specification." MPEP 2111. “Under a broadest reasonable interpretation (BRI), words of the claim must be given their plain meaning, unless such meaning is inconsistent with the specification.” MPEP 2111.01(I).
“Biological absorption” is understood as stating that CO2 is “absorbed,” i.e. incorporated into a biological system/cell, which indicates that CO2 is metabolized by a biological cell such that CO2 is transformed into a different compound(s) by biological activity, i.e. into the biomass of the cell or otherwise. The preamble of claim 15 is considered to be limiting in that “biological absorption” must occur. The plain meaning of the statement “process for the biological production of hydrogen . . . by biological absorption of carbon dioxide” is that such biological production is caused or brought about “by” biological absorption, such that the claims appear to directly encompass a direct mechanistic link between biological absorption (i.e. metabolism) of CO2 and hydrogen production. It is noted that at least claim 15 does not require production of methane nor any involvement of a methanogenic microorganism, wherein production of methane and a third reactor containing a methanogenic microorganism is recited in the alternative as part of a Markush group.
A complete embodiment of claim 15 requires only the recited first reactor with hydrogen-producing bacteria and a second reactor with an acetogenic microorganism. As will be discussed in greater detail below, hydrogen-producing bacteria have no ability to biological absorb (i.e. metabolize) CO2 while acetogenic bacteria absorb CO2 and hydrogen to produce acetate through the Wood-Ljungdahl pathway. As such, the broadest reasonable interpretation of claim 15 also includes embodiments wherein biological absorption of CO2 is done only by the recited acetogenic bacteria in the second reactor.
It is noted that this rejection may be overcome by clarifying in the claims that biological absorption of CO2 produces methane or supports the acetogenic bacteria and or otherwise clarifying that biological absorption does not occur in the first reactor.
Carbon dioxide does not have any hydrogen atoms that may be converted to molecular hydrogen (H2). Regardless, recitation of a first or second culture medium implies that such medium has appropriate composition, which can include carbohydrates, suitable for maintenance of the recited bacteria including maintenance for a hydrogen-producing bacteria to produce hydrogen as recited in claim 15.
The physiology of hydrogen-producing bacteria to produce hydrogen is well understood in the prior art. For example, Singer et al. (Anaerobic membrane gas extraction facilitates thermophilic hydrogen production from Clostridium thermocellum, Environ. Sci. Water Res. Technol. 4, 2018, 1771), Fig. 5, shows that the hydrogen producing bacterium Clostridium (Hungateiclostridium) thermocellum produces hydrogen by extracting reducing equivalents (electron flow in Fig. 5) from carbohydrate/cellulose through the well-understood process of glycolysis that drives the production of H2 (by reduction of H+). CO2 is fully oxidized and cannot serve as a source of electrons to drive the production H2. There is no report nor any evidence of record nor the specification of the ability of any hydrogen-producing bacteria as recited in claim 15 to biologically absorb carbon dioxide in a process of biological production of H2.
Similarly, the metabolism of Moorella thermoacetica and other acetogenic bacteria to utilize CO2 as a carbon source is well-described in the prior art. Huang et al. (Electron Bifurcation Involved in the Energy Metabolism of the Acetogenic Bacterium Moorella thermoacetica Growing on Glucose or H2 plus CO2, J. Bacteriol. 194, 2012, 3689-99), Fig. 1, shows that M. thermoacetica and other acetogens has the ability to reduce CO2 to acetate (and possibly other products) wherein H2 can serve as a source of reducing equivalents as shown in Equation 8 of Huang:
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43
387
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However, the above equation is not biological production of hydrogen by biological conversion of carbon dioxide as recited but rather biological consumption of hydrogen to reduce carbon dioxide to acetate.
The specification contains no working examples and no theoretical discussion regarding how a hydrogen-producing bacterium and/or an acetogenic bacterium as recited carry out biological absorption of carbon dioxide to biologically produce hydrogen as recited.
As such, the evidence of record shows the following:
The genus of hydrogen-producing bacteria/microorganism recited in claim 15 does not perform, is not known in the evidence of record to perform, and/or is not demonstrated in the specification to perform biological production of hydrogen by biological absorption of carbon dioxide;
The genus of acetogenic bacteria recited in claim 15 does not perform, is not known in the evidence of record to perform, and/or is not demonstrated in the specification to perform biological production of hydrogen by biological absorption of carbon dioxide; and
By extension of the above a combination of a hydrogen-producing bacteria and an acetogenic bacteria as recited is not known in the evidence of record to perform, and/or is not demonstrated in the specification to perform biological production of hydrogen by biological absorption of carbon dioxide.
However, it is noted that acetogenic bacteria biologically absorb hydrogen and carbon dioxide to produce acetate, and methanogenic microorganism biologically absorb hydrogen and carbon dioxide to produce methane, as reviewed above.
“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.” Here, none of the recited genera of bacteria are understood to have an ability to biologically absorb carbon dioxide to biologically produce hydrogen as recited. That is, the claims recite a new and novel metabolic activity for the recited bacteria to produce hydrogen by biological absorption of carbon dioxide, and the specification lacks an adequate written description that would allow for an ordinarily skilled artisan at the time of filing to recognize possession that any process involving hydrogen-producing bacteria, acetogenic bacteria or combinations as recited has the required function for biological absorption of carbon dioxide to biologically produce hydrogen.
In the interest of compact prosecution, any role of CO2 in assisting in fermentation and hydrogen production by a hydrogen-producing bacterium as recited will be considered to meet the features of claims even if such CO2 does not undergo chemical change directly leading to hydrogen production (i.e. CO2 used as a sparging gas to assist in anaerobic conditions or to maintain a buffer, e.g. formation of bicarbonate), or is absorbed only by the recited acetogenic bacteria.
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) 15, 21-24 and 27-28 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bothun et al. (Metabolic selectivity and growth of Clostridium thermocellum in continuous culture under elevated hydrostatic pressure, Appl. Microbiol. Biotechnol. 65, 2004, 149-157) further in view of Huang et al. (Electron Bifurcation Involved in the Energy Metabolism of the Acetogenic Bacterium Moorella thermoacetica Growing on Glucose or H2 plus CO2, J. Bacteriol. 194, 2012, 3689-99), Rabemonolontsoa et al. (Effects of gas condition on acetic acid fermentation by Clostridium thermocellum and Moorella thermoacetica (C. thermoaceticum), Appl. Microbiol. Biotechnol. 2017, DOI 10.1007/s00253-017-8376-4) and Bakonyi et al. (Escherichia coli (XL1-BLUE) for continuous fermentation of bioH2 and its separation by polyimide membrane, Int. J. Hydrogen Energy 37, 2012, 5623-30).
As an initial matter, it is noted that Clostridium thermocellum and Hungateiclostridium thermocellum are the same organism.
Bothun, abstract, states:
The continuous culture of Clostridium thermocellum, a thermophilic bacterium capable of producing ethanol from cellulosic material, is demonstrated at elevated hydrostatic pressure (7.0 MPa, 17.3 MPa) and compared with cultures at atmospheric pressure. A commercial limitation of ethanol production by C. thermocellum is low ethanol yield due to the formation of organic acids (acetate, lactate). At elevated hydrostatic pressure, ethanol:acetate (E/A) ratios increased >102 relative to atmospheric pressure. Cell growth was inhibited by approximately 40% and 60% for incubations at 7.0 MPa and 17.3 MPa, respectively, relative to continuous culture at atmospheric pressure. A decrease in the theoretical maximum growth yield and an increase in the maintenance coefficient indicated that more cellobiose and ATP are channeled towards maintaining cellular function in pressurized cultures. Shifts in product selectivity toward ethanol are consistent with previous observations of hydrostatic pressure effects in batch cultures. The results are partially attributed to the increasing concentration of dissolved product gases (H2, CO2) with increasing pressure; and they highlight the utility of continuous culture experiments for the quantification of the complex role of dissolved gas and pressure effects on metabolic activity.
“Continuous culture experiments at atmospheric pressure (0.1 MPa) were performed at 333 K with a MultiGen fermentor (345 ml working volume; New Brunswick). After inoculation, the system was kept in batch mode for 24 h before initiating a continuous flow of medium. Deoxygenated medium containing cellobiose at 2 g l−1 was fed into the fermenter using a peristaltic pump (LKB Pharmacia) to achieve the desired dilution rate (D=0.05–0.32 h−1). Samples were taken from the reactor at steady-state, which was defined as 98% turnover of the culture vessel contents. The cell culture was continuously stirred using an impeller (300 rpm) and deoxygenated CO2 was used to sparge the bicarbonate-buffered system. Product gases and sparging CO2 were vented to maintain atmospheric pressure. The results of the continuous culture at atmospheric pressure are based on multiple chemical analyses of duplicated experiments conducted independently.” Bothun, page 150, right col.
The statement that “Product gases and sparging CO2 were vented to maintain atmospheric pressure” indicates that sparging gas was introduced during culturing, which is also suggested by the pressurized system in Fig. 1 of Bothun. Regardless, introduction of at least an initial CO2 sparge gas satisfies the claim limitation of “introducing carbon dioxide into at least one first reactor.”
“C. thermocellum produces gaseous end-products (H2, CO2).” Bothun, page 150, left col. “Although H2 and CO2 formation were not determined experimentally, their concentrations in the fermentation broth were calculated using a metabolic flux analysis. Assuming equilibrium conditions in the mixed vessel, the H2 formed in continuous culture at atmospheric pressure ([H2]aq=15.6–38.3 mM, as a function of the dilution rate) primarily evolved into the headspace. “ Bothun, page 153, left col. As such, while Bothun discusses the production of ethanol and acetate, H2 is necessarily produced in the headspace of the fermenter wherein product gasses are vented as discussed above.
Fig. 2 of Bothun (triangle at 0.1 MPa) shows cell density as a function of various dilution rates trialed in continuous culture indicates that the cell density is steady during culture, which directly suggests that a stationary phase is reached during continuous culture. That is, an ordinarily skilled artisan at the time of filing would recognize from Fig. 2 of Bothun that cells cannot be a continued growth phase but must reach a stationary phase with a stable cell density.
As such, Bothun discloses the following method:
A process for the biological production of hydrogen by introducing a carbon dioxide sparging gas in a first reactor containing a first culture medium comprising Hungateiclostridium thermocellum and keeping under continuous stirring in anaerobic conditions (i.e. N2 gas sparging) until a stationary phase of growth of Hungateiclostridium thermocellum is achieved, obtaining a first fermented culture medium (see discussion of residual cellobiose in Fig. 2A of Bothun wherein a fermented medium is necessarily produced) and a gaseous mixture of hydrogen and residual CO2 (as a product and from sparging gas) is produced.
However, Thompson does not teach the features associated with a second reactor as recited in claim 15.
The production of hydrogen by biological fermentation is recognized in the prior art as a valuable product. Bakonyi, abstract, discusses hydrogen production by E. coli wherein such produced hydrogen is collected and purified with a gas separation membrane. “In membrane gas separation the gas to be separated is introduced on the feed side of membrane and then separated into two main fractions, the permeate and the retentate.” Bakonyi, sec. 2.4. “The experiments regarding H2/CO2 separation were performed in a laboratory scale membrane testing device, equipped with pressure indicators and digital gas flow meters as well as various valves that allow precise measurement control.” Bakonyi, page 5626, left col. Since any gas would disperse into the atmosphere if not contained in a suitable vessel, an ordinarily skilled artisan at the time of filing would have understood that it is advantageous to collect produced hydrogen so the same can be used wherein any collection vessel is within the broadest meaning of an accumulation tank. “[B]iological hydrogen production methods from easily available, cheap, renewable resources take place under nearly ambient conditions and thus, offer promising way to replace conventional methods.” Bakonyi, pages 5623-24. As such, it is clear that hydrogen produced from biological sources a separated as described is meant to be used as a valuable product that would suggest its storage in a suitable vessel. Fig. 1 of Bakonyi shows the production of separate permeate fraction 14 and retentate fractions 17 that represent output of separated hydrogen and carbon dioxide.
While Bakonyi and Bothun utilize different organisms for producing hydrogen by fermentation, at the time of filing an ordinarily skilled artisan would have been motivated to collect any hydrogen otherwise wasted by venting to the atmosphere as taught by Bothun and separate such hydrogen using a membrane from carbon dioxide since Bakonyi teaches that such bio-hydrogen is a valuable product and suitable for the same uses as hydrogen produced from conventional sources.
Huang, abstract, teaches:
Moorella thermoacetica ferments glucose to three acetic acids. In the oxidative part of the fermentation, the hexose is converted to 2 acetic acids and 2 CO2 molecules with the formation of 2 NADH and 2 reduced ferredoxin (Fdred2−) molecules. In the reductive part, 2 CO2 molecules are reduced to acetic acid, consuming the 8 reducing equivalents generated in the oxidative part. An open question is how the two parts are electronically connected, since two of the four oxidoreductases involved in acetogenesis from CO2 are NADP specific rather than NAD specific. We report here that the 2 NADPH molecules required for CO2 reduction to acetic acid are generated by the reduction of 2 NADP+ molecules with 1 NADH and 1 Fdred2− catalyzed by the electron-bifurcating NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (NfnAB). The cytoplasmic iron-sulfur flavoprotein was heterologously produced in Escherichia coli, purified, and characterized. The purified enzyme was composed of 30-kDa (NfnA) and 50-kDa (NfnB) subunits in a 1-to-1 stoichiometry. NfnA harbors a [2Fe2S] cluster and flavin adenine dinucleotide (FAD), and NfnB harbors two [4Fe4S] clusters and FAD. M. thermoacetica contains a second electron-bifurcating enzyme. Cell extracts catalyzed the coupled reduction of NAD+ and Fd with 2 H2 molecules. The specific activity of this cytoplasmic enzyme was 3-fold higher in H2-CO2-grown cells than in glucose-grown cells. The function of this electron-bifurcating hydrogenase is not yet clear, since H2-CO2-grown cells additionally contain high specific activities of an NADP+-dependent hydrogenase that catalyzes the reduction of NADP+ with H2. This activity is hardly detectable in glucose-grown cells.
“M. thermoacetica cells were grown at 55°C on H2-CO2 in 2-liter glass bottles containing 500 ml of medium and 80% H2–20% CO2 as the gas phase at 1.3 x 105 Pa. The medium was the same as that described above for growth on glucose, with exceptions that it did not contain glucose and that the concentrations of tryptone and yeast extract were only 2 g per liter. After inoculation with 50 ml of a glucose-grown preculture, the culture was allowed to grow for about 1 week until it no longer took up H2, as measured manometrically.” Huang, page 3691, left col. The statement “until no longer took up H2” is understood as a statement that H2 is still present, but is no longer being utilized.
As such, Huang teaches:
A method of producing a product (acetic acid) by introducing into a (second) bioreactor having a culture medium comprising M. thermoacetica under anaerobic conditions a mixture of hydrogen and carbon dioxide and obtaining a second cultured medium and hydrogen, such hydrogen being any unconsumed hydrogen.
The structure and chemical nature of CO2 and hydrogen is the same regardless of how it is produced. Huang does not specify the source of carbon dioxide and hydrogen used for culture of M. thermoacetica. However, at the time of filing an ordinarily skilled artisan would have been motivated to employ any conveniently available source of carbon dioxide and hydrogen including carbon dioxide and hydrogen produced by the culture of H. thermocellum taught by Bothun. Again, Bothun teaches that the sparging gas carbon dioxide is vented. This vented mixture of carbon dioxide and hydrogen can be collected and applied to any further useful purpose, particularly since hydrogen in particular is valuable and useful product. As far as such vented mixture of carbon dioxide and hydrogen may not have a suitable ratio of carbon dioxide to hydrogen for the methods of Huang, just as Huang has an alternative source of carbon dioxide and hydrogen the carbon dioxide and hydrogen collected from a culture of H. thermocellum can be supplemented with additional carbon dioxide or hydrogen to reach a proper ratio.
Further, it is known in the prior art to utilize hydrogen produced by H. thermocellum to drive acetic acid production by M. thermoacetica. Rabemonolontsoa et al., abstract, teach co-cultures of C. thermocellum and Moorella thermoacetica (an acetogenic bacterium). “Increased acetic acid concentration, superior to the theoretical maximum, was obtained with sparged CO2 in co-culture using glucose and cellobiose as substrates, but not in monoculture. M. thermoacetica is able to synthesize acetic acid from CO2 through acetyl-CoA BWood–Ljungdahl^ pathway. Electron donors such as H2 or CO are necessary for such synthesis. . . . C. thermocellum produces electron donors, for instance H2 as one of its end-products.” As shown in Fig. 5 of Rabemonolontsoa, H2 produced by C. thermocellum can serve as reducing equivalents for M. thermoacetica to produce acetic acid. While Rabemonolontsoa focuses on co-cultures, Huang teaches that M. thermoacetica can be cultured alone to produce acetic acid provided that exogenous hydrogen and carbon dioxide is supplied. Rabemonolontsoa teaches that hydrogen produced by M. thermoacetica is suitable for provision of reducing equivalents for acetic acid production by M. thermoacetica such that an ordinarily skilled artisan at time of filing would have recognized that a culture of C. thermocellum can successfully serve as a suitable source of hydrogen and carbon dioxide for a culture of M. thermoacetica, wherein carbon dioxide and hydrogen for culturing M. thermoacetica as taught by Huang must necessarily be obtained from some source. Upon making such combination all features of claims 15 and 22 and are met except for continuous stirring of the second reactor.
Regarding continuous stirring of the second reactor (reactor taught by Huang), as discussed, Bothun discusses culturing under continuous stirring conditions. That is, an ordinarily skilled artisan at the time of filing would have been motived to continuously stir any culture of cells, for example, to assist in the dispersion of hydrogen/carbon dioxide introduced to the culture of Huang into the culture medium.
Regarding recitation that the first and second reactors contain up to 95% of the respective first and second reactors, Bothun does not specify the volume of culture medium placed in a MultiGen fermenter with a 345 ml working volume. However, discussion of a “headspace” indicates that the fermenter/reactor is not 100% full of culture media. Huang, page 3690, right col., specifies 500 mL of medium in a 2 liter vessel/reactor or 25% by volume. As such, Huang teaches that it is well established in the prior art to have a culture medium take up less than 95% by volume of reactor; since Bothun indicates the presence of a “headspace,” at the time of filing an ordinarily skilled artisan would be well informed that utilization of less than 95% of the reactor space filled with culture medium would be an appropriate manner to perform the atmospheric pressuring fermentation of H. thermocellum taught by Bothun.
Regarding claim 21, upon recovery of carbon dioxide and hydrogen from the fermentation taught by Bothun, an ordinarily skilled artisan would have readily understood that the same must be collected in some sort of suitable vessel to prevent dispersal into the atmosphere. Any such container is within the broadest meaning of an accumulation tank.
Regarding claim 23, as discussed above, Bakonyi teaches that it is advantageous to separate hydrogen from carbon dioxide from a fermentation production the same by membrane separation, which also necessarily produces a second carbon dioxide product (e.g. retentate and permeate fractions as discussed). After obtaining such hydrogen and carbon dioxide, an ordinarily skilled artisan at time of filing would have been motivated to apply such hydrogen and carbon dioxide to any and uses to which hydrogen can be applied. As far as culturing of M. thermoacetica as taught by Huang may require specific ratios of hydrogen to carbon dioxide, an ordinarily skilled artisan would have been motivated to mix such purified carbon dioxide and hydrogen (separated from the fermentation of Bothun) in a suitable ratio and apply the same as the source of carbon dioxide and hydrogen to the fermentation in a second reactor taught by Huang as discussed above, since a suitable mixture of carbon dioxide and hydrogen must be supplied and the prior art including Bakonyi teaches that bioproduced hydrogen is a particularly economical source of hydrogen.
Regarding claim 24 Huang does not necessarily teach that a mixture of carbon dioxide and hydrogen is injected in a culture media rather than just provided in a head space and allowed to diffuse. However, when introducing gas to culture, it is well known in the art that such gas can be injected or “bubbled” into a culture medium. For example, Rabemonolontsoa, Fig. 1, shows a culture set up wherein an input gas is injected into the culture medium “gas bubbling.” In the absence of any specific unexpected result, it is not inventive to introduce a gas, including any mixture of carbon dioxide and hydrogen discussed above, into a cell culture by injecting the same into a culture medium or the headspace of a reactor.
Regarding claim 27, Huang teaches that cultured M. thermoacetica are valuable to recover after culturing discussing “cells harvested by centrifugation under N2.” Huang, page 3691, right col. After culturing M. thermoacetica in the presence of a mixture of hydrogen and carbon dioxide as discussed above, it is not inventive to recover the M. thermoacetica such cultured by centrifugation or otherwise, such separation of cells from a fermented liquid culture medium being separating into a liquid component and a solid component.
Regarding claim 28, as discussed, Huang teaches the provision of both hydrogen and carbon dioxide that do not originate from step (i) as recited. As far as a specific ratio of hydrogen and carbon dioxide is required by the methods of Huang as discussed above, an ordinarily skilled artisan at the time of filing would have been motivated to adjust the ratio of carbon dioxide and hydrogen in a mixture obtained from a fermentation to have a proper ratio by addition of carbon dioxide and/or hydrogen from any source including one that does not originate from a fermentation as recited in step (i).
Claim(s) 15, 21-24 and 27-29 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bothun et al. (Metabolic selectivity and growth of Clostridium thermocellum in continuous culture under elevated hydrostatic pressure, Appl. Microbiol. Biotechnol. 65, 2004, 149-157), Huang et al. (Electron Bifurcation Involved in the Energy Metabolism of the Acetogenic Bacterium Moorella thermoacetica Growing on Glucose or H2 plus CO2, J. Bacteriol. 194, 2012, 3689-99), Rabemonolontsoa et al. (Effects of gas condition on acetic acid fermentation by Clostridium thermocellum and Moorella thermoacetica (C. thermoaceticum), Appl. Microbiol. Biotechnol. 2017, DOI 10.1007/s00253-017-8376-4) and Bakonyi et al. (Escherichia coli (XL1-BLUE) for continuous fermentation of bioH2 and its separation by polyimide membrane, Int. J. Hydrogen Energy 37, 2012, 5623-30) as applied to claims 15, 21-24 and 27-28 above, and further in view of Hu et al. (Integrated bioprocess for conversion of gaseous substrates to liquids, PNAS 113, 2016, 3773-78).
Regarding claim 29, Huang teach culturing of M. thermoacetica in a sealed container/reactor. However, growth of M. thermoacetica in a reactor wherein a mixture of hydrogen and carbon dioxide is continuously supplied is known in the prior art.
Hu, abstract, teaches “an anaerobic bioreactor converts mixtures of gases of CO2 and CO or H2 to acetic acid, using the anaerobic acetogen Moorella thermoacetica,” wherein produced acetic acid is then converted to lipids by downstream Yarrowia lipolytica in a separate reactor. Regardless of the specifics of Hu, Hu teaches that M. thermoacetica can be adequately cultured by providing a continuous stream of carbon dioxide and hydrogen: “Fermentation was carried out at a flow rate of 1,000 standard cubic centimeters per minute (sccm), using either CO or H2 as reducing gas at a composition of 7/3 CO/CO2 or 7/3 H2/CO2.” Hu, page 3774, left col. This is a description of continuously introducing a mixture of hydrogen and carbon dioxide to a reactor for growing M. thermoacetica for acetic acid production. As such, at the time of filing, an ordinarily skilled artisan would have been motivated to utilize any means for culturing M. thermoacetica with hydrogen and carbon dioxide for acetic acid production with an expectation of success, whether using a fixed atmosphere of hydrogen and carbon dioxide as taught by Huang or by introducing a continuous flow hydrogen and carbon dioxide as taught by Hu.
Claim(s) 15-17, 21-24 and 27-28 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bothun et al. (Metabolic selectivity and growth of Clostridium thermocellum in continuous culture under elevated hydrostatic pressure, Appl. Microbiol. Biotechnol. 65, 2004, 149-157), Huang et al. (Electron Bifurcation Involved in the Energy Metabolism of the Acetogenic Bacterium Moorella thermoacetica Growing on Glucose or H2 plus CO2, J. Bacteriol. 194, 2012, 3689-99), Rabemonolontsoa et al. (Effects of gas condition on acetic acid fermentation by Clostridium thermocellum and Moorella thermoacetica (C. thermoaceticum), Appl. Microbiol. Biotechnol. 2017, DOI 10.1007/s00253-017-8376-4) and Bakonyi et al. (Escherichia coli (XL1-BLUE) for continuous fermentation of bioH2 and its separation by polyimide membrane, Int. J. Hydrogen Energy 37, 2012, 5623-30) as applied to claims 15, 21-24 and 27-28 above, and further in view of Zhao et al. (Hydrogen production by the newly isolated Clostridium beijerinckii RZF-1108, Bioresource Tech. 102, 2011, 8432-36).
Regarding claims 16 and 17, Bothun (first reactor) and Huang (second reactor) teach pressures less than 250 kPa. Specifically, Bothun teaches 0.1 MPa (100 kPa) and Huang teaches 1.3 x 105 Pa (130 kPa). However, both Bothun and Huang teach temperatures greater than 40[Symbol font/0xB0]C (claim 16) and 39[Symbol font/0xB0]C (claim 16), specifically at about 60[Symbol font/0xB0]C in Bothun and 55[Symbol font/0xB0]C in Huang.
“Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical.” “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." MPEP 2144.05(II)(A). Here, it is known in the art to culture cells at different temperatures. Zhao, Fig. 2, shows the effect of culture temperature on cultures of C. beijerinckii showing that although there may be an optimum temperature for product formation, Clostridium cells can grow under a range a range of temperatures. An ordinarily skilled artisan at the time of filing would have expected that many different types of cells including H. thermocellum and M. thermoacetica can grow at multiple temperatures and it is not inventive discover that any particular cell can be cultured at a temperature of less than 40[Symbol font/0xB0]C or 39[Symbol font/0xB0]C.
Claim(s) 15, 19-24 and 27-28 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bothun et al. (Metabolic selectivity and growth of Clostridium thermocellum in continuous culture under elevated hydrostatic pressure, Appl. Microbiol. Biotechnol. 65, 2004, 149-157), Huang et al. (Electron Bifurcation Involved in the Energy Metabolism of the Acetogenic Bacterium Moorella thermoacetica Growing on Glucose or H2 plus CO2, J. Bacteriol. 194, 2012, 3689-99), Rabemonolontsoa et al. (Effects of gas condition on acetic acid fermentation by Clostridium thermocellum and Moorella thermoacetica (C. thermoaceticum), Appl. Microbiol. Biotechnol. 2017, DOI 10.1007/s00253-017-8376-4) and Bakonyi et al. (Escherichia coli (XL1-BLUE) for continuous fermentation of bioH2 and its separation by polyimide membrane, Int. J. Hydrogen Energy 37, 2012, 5623-30) as applied to claims 15, 21-24 and 27-28 above, and further in view of Dolejs et al. (Butanol production by immobilised Clostridium acetobutylicum in repeated batch, fed-batch, and continuous modes of fermentation, Bioresource Technol. 169, 2014, 723-30).
Regarding claims 19 and 20, as discussed above, Bothun discusses a continuous fermentation. However, other modes of culturing anaerobic Clostridium bacteria are known in the prior art. Dolejs discusses culturing of Clostridium acetobutylicum, both free cell and immobilized on a polyvinylalcohol hydrogel, by continuous, repeated batch and fed-batch fermentations. For repeat batch fermentations, Dolejs, page 724, right col., teaches the following:
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Many standard culture techniques are known in the prior art for Clostridium bacteria. Both continuation fermentation and repeat batch fed fermentation are known in the prior art to extend the length of time of culture while using the same cells. Which technique that an ordinarily skilled artisan at the time of filing would chose is a matter of convenience (e.g. which equipment is readily available) and design choice that are expected to be successful in culture Clostridium bacteria. As such, it is not inventive for an ordinarily skilled artisan at the time of filing to culture H. thermocellum (C. thermocellum) as taught by Bothun by an alternative means of repeat bath fermentation. It is noted that Dolejs, sec. 2.2, teaches the need to sparge culture media with N2; however, as discussed, Bothun teaches that the specific media taught by Bothun should be sparged with carbon dioxide.
As above in the text quoted from Dolejs, culture by repeat batch fermentation involves after depletion of media, includes unloading from a first reactor the volume of first fermented culture medium in a manner that the cells are retained with the reactor. In this way, the concentration of cells in terms of weight per liter volume of remaining fermented media is increased. Replacing the drained fermented medium with fresh medium, wherein an ordinarily skilled artisan at time of filing would have no reason to use a different volume of culture medium different from the volume used in the first instance of batch culturing. And then restarting growth that includes reaching a stationary phase as far as Fig. 2 of Bothun teaches that cells are expected to reach a fix cell density. Regarding recitation of a concentration of cells of no less than 2 g/l is reached, Fig. 2B of Bothun teaches that the concentration of cells in media is expected to be about 0.5 g/L. As such, upon draining the majority of volume of fermented first medium while maintaining the cells in the reactor, it would be fully expected by an ordinarily skilled artisan at time of filing that a cell concentration of at least 2 g/L will be reached, for example by draining at least 75% of the volume of first fermented medium (Dolejs suggest drain substantially all of the old fermented media). Dolejs teaches that these steps can be repeated many time. Since an ordinarily skilled artisan at the time of filing would have been motivated to culture the H. thermocellum of Bothun though any well-established means, an ordinarily skilled artisan would have been motivated to do the above as to meet the features of claim 19. Regarding claim 20, the “sieving” to separate immobilized cells from the first fermented media described by Dolejs is separation of the first fermented medium into a liquid component and a solid component (the cells).
Allowable Subject Matter
Claims 25 and 26 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
The following is a statement of reasons for the indication of allowable subject matter:
Claim 25 requires a methane containing gas from the recited third reactor be introduced into a second reactor containing an acetogenic bacterium, wherein such gas will further be depleted in CO2 due to activity of the methanogenic organism in the third reactor. As discussed above, an acetogenic bacteria in additional to having ability to metabolize carbohydrates can produce acetate (and other products) by reduction of CO2 with H2. Acetogens as recited in claim 15 have no known ability to utilize methane in any productive fashion. It is known in the art that a class of microorganisms known as methanotrophs that can utilize methane through activity of a methane monooxygenase. However, there is no apparent technical reasons to specifically introduce a methane-containing gas to a reactor that does not contain a methanotroph nor is there a particular reason to combine an acetogenic microorganism and a methanotroph into the same second reactor.
Response to arguments
Regarding claim rejections under 35 U.S.C. 112(a), the amended claim language is addressed above. Regarding applicant’s statement:
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Claim 15 directly recites biological absorption of CO2 for biological production of hydrogen, as discussed above.
Applicant argues:
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C. thermocellum cannot produce ethanol without producing hydrogen, wherein hydrogen ion (i.e. hydrogenase activity) is the final electron receptor for the metabolism of C. thermocellum. “C. thermocellum produces gaseous end-products (H2, CO2).” Bothun, page 150, left col. This is a teaching that C. thermocellum always produces hydrogen gas. “Product gases [e.g. hydrogen] and sparging CO2 were vented to maintain atmospheric pressure.” Bothun, page 150, right col. Bothun teaches that the formation of product gases including hydrogen cannot be stopped, but hydrogen can be removed by venting to atmosphere. As such, Bothun in all of its embodiments is a method for biological production of hydrogen. Any ethanol production by C. thermocellum is proportional to hydrogen production. “[I]n order for C. thermocellum to produce a single acetate molecule (with a concomitant ATP molecule), two H2 gas molecules must also be formed, so that an oxidation/reduction balance is maintained.” Bothun, page 155, right col. Further, Bothun, page 155, right col, directly describes increased hydrogen levels as beneficial for production of ethanol:
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Applicant argues:
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“H2 formed in continuous culture at atmospheric pressure ([H2]aq=15.6–38.3 mM, as a function of the dilution rate) primarily evolved into the headspace.” Bothun, page 153, left col. Embodiments of Bothun wherein carbon dioxide and hydrogen are vented to atmosphere at atmospheric pressure are relied upon for the rejection. Embodiments under 7.0 MPa pressure wherein hydrogen will remain dissolved are not relied upon.
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In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., see below) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
Claims recite biological absorption (i.e. biological metabolism) of carbon dioxide, which is not an “inert” use. The present rejections are only made since the applicant may intend, but is not actively claiming an inert use of CO2, since it is impossible for a hydrogen producing bacteria to biological absorb carbon dioxide for biological production of hydrogen. However, Bothun teaches an inert use of CO2 (sparging), which is why the rejection is made in the interest of compact prosecution. The claims require only stirring, which applicant states is taught by Bothun. The claims are not limited to an intention of such stirring to increase hydrogen production. Bothun teaches that at atmospheric pressure hydrogen accumulates in the headspace in gas phase and is vented to atmosphere and not dissolved.
Applicant argues:
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In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., pure hydrogen) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
Nothing in the claims requires purified hydrogen (99.9% or otherwise) not hydrogen meeting any ISO standard. Rather, the claims require impure hydrogen that is mixed with carbon dioxide. Bakonyi is cited only for stating that technology to purify (i.e. any increase in concentration) hydrogen from a hydrogen and carbon dioxide mixture is generally extant in the prior art. There is nothing in the claims to require production of 65% hydrogen and 35% CO2 without a membrane wherein the claims explicitly recite “optionally separating the hydrogen from the gaseous mixture,” which includes doing the same with a membrane or by any other means, which indicates that a specific gas content need not be produced by the first reactor.
Applicant argues:
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“Up to 95%” includes all values less than 95%, such as 0.1%, 1% and 75% of reactor capacity.
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Huang is cited for showing that it is known to utilize biologically produced hydrogen to support culturing of an acetogenic microorganism and for nothing more. The same is evident by hydrogen having the same structure regardless of its means of production. That is, hydrogen as a biproduct of natural gas extraction and from fermentation are chemically identical.
Rabemonolontsoa is cited for showing the M. thermoacetica utilizes hydrogen and not for hydrogen production.
Applicant argues:
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Zhao is cited to show only that it is known that clostridium cells do not have strict temperature requirements wherein discovery of workable temperatures is not inventive as supported by MPEP 2144.05(II)(A) outside showing that the claimed temperature is critical for functionality.
Applicant argues:
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Dolejs teaches a culture method in which cells can be reused upon exhaustion of a culture medium. The motivation is to save material cost by reusing already cultured cells by retaining the cells in a reactor while the media is replaced with fresh media.
Conclusion
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.
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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