DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
Receipt of Arguments/Remarks filed on 11/13/2025 is acknowledged. Claims 1-3 and 7-25 are pending. Claims 1 and 7-13 were amended. Claims 4-6 were canceled. Claims 14-25 are withdrawn as being directed to a nonelected invention. Claims 1-3 and 7-13 are under examination herein.
Withdrawn Objections/Rejections
The objections to the drawings and to claims 1, 4-7, 9 and 11-13 are withdrawn.
The rejection of claim 13 under 35 U.S.C. § 112(b) is withdrawn.
New, maintained, and modified rejections necessitated by amendment
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 1-3 and 7-12 are rejected under 35 U.S.C. 103 as being unpatentable over Scaife et al., US 9,873,880 B2 in view of Damude US 2011/0086919 A1.
Regarding claim 1, Scaife teaches a process for producing polyunsaturated fatty acids (PUFAs) using a recombinant microorganism (Scaife claims 29-37). Scaife exemplifies an engineered Thraustochytrium cell, but also teaches that various microalgae can be used as host cells in the methods of producing PUFAs, including Chlorella protothecoides, now known as Auxenochlorella protothecoides (Scaife col. 26 line 9). Scaife teaches a method involving an engineered microorganism containing at least one heterologous enzyme-encoding polynucleotide which encodes an elongase and a desaturase (Scaife claim 35). Scaife teaches that the desaturase is a delta-5 desaturase (Scaife claim 27). Scaife teaches culturing the microorganism to produce polyunsaturated fatty acids (Scaife claim 33).
Regarding claims 2 and 3, Scaife teaches that the fatty acid can include arachidonic acid (ARA) or eicosapentaenoic acid (EPA) (Scaife claim 34).
Scaife does not teach that the elongase is delta-9 elongase (claim 1), that the delta-9 elongase is from the group consisting of Euglena gracilis, Isochrysis galbana, and Pavlova pingui (claim 1), that the delta-8 desaturase is from the microorganisms set forth in claim 7, that the delta-8 desaturase converts EDA to DGLA (claim 8), that the delta-5 desaturase is from the microorganisms set forth in claim 9, that delta-5 desaturase enzymes convert DGLA to ARA (claim 10), that the delta-17 desaturase is from the microorganisms set forth in claim 11, or that delta-17 desaturase enzymes convert ARA to EPA (claim 12).
Regarding claim 1, Damude teaches recombinant Yarrowia sp. for production of EPA comprising a gene encoding delta-9 elongase (Damude claim 3). Damude teaches the delta-9 elongase is from Isochrysis galbana (Damude pg. 40 para 416). Damude teaches recombinant Yarrowia comprising delta-8, delta-5, and delta-17 desaturase (Damude claim 24).
Regarding claim 7, Damude teaches delta-8 desaturase from Euglena gracilis (Damude pg. 40 para. 417).
Regarding claim 8, Damude teaches that delta-8 desaturases catalyze the conversion of EDA to DGLA (Damude pg. 24 para. 280).
Regarding claim 9, Damude teaches delta-5 desaturase from M. alpina (Damude pg. 39 para 402).
Regarding claim 10, Damude teaches that delta-5 desaturases catalyze the conversion of DGLA to ARA (Damude pg. 24 para. 280).
Regarding claim 11, Damude teaches delta-17 desaturase from Saprolegnia diclina (Damude pg 39 para 405).
Regarding claim 12, Damude teaches that delta-17 desaturases catalyze the conversion of ARA to EPA (Damude pg. 24 para. 280).
It would have been obvious to a skilled artisan, before the effective filing date, to combine the teachings of Scaife and Damude, resulting in a process of producing polyunsaturated fatty acids (PUFAs) as instantly claimed. Both Scaife and Damude teach the production of PUFAs using recombinant microorganisms expressing desaturases and elongases. It would have been obvious to a skilled artisan that the specific elongases and desaturases taught by Damude could be incorporated into an Auxenochlorella protothecoides strain as taught by Scaife.
A person of ordinary skill in the art would have been motivated to combine the teachings of Scaife and Damude and create a strain incorporating delta-9 elongase and the desaturases taught by Damude because each of these enzymes catalyze different steps in the fatty acid biosynthetic pathway leading to the production of numerous fatty acids of interest, such as EDA to DGLA (delta-8 desaturase), DGLA to ARA (delta-5 desaturase), or ARA to EPA (delta-17 desaturase) (Damude Fig. 1). Therefore, as demonstrated by Damude, it is advantageous for industrial production of PUFAs to be able to manipulate and metabolically engineer multiple steps in the biosynthetic pathway (Damude “Background of the Invention”).
A skilled artisan would have a reasonable expectation of success in combining these teachings to achieve the predictable outcome of a recombinant A. protothecoides strain for PUFA production as instantly claimed, given the teachings of Scaife and Damude that the claimed elongase and desaturase enzymes can be incorporated into various microorganisms for engineered production of PUFAs. As Scaife teaches the expressing elongases and desaturases in host cells for PUFA production, and further teaches that a host cell for this process may be Chlorella protothecoides (A. protothecoides), a skilled artisan could reasonably expect success in expressing the specific elongases and desaturases taught by Damude in such a strain.
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Scaife in view of Damude as applied to claims 1-3 and 7-12 above, and further in view of Yazawa et al., Applied microbiology and biotechnology; 87:2185-93.
Scaife and Damude teach the process of claim 1 as set forth above. Damude teaches a recombinant microorganism for fatty acid production that comprises genes encoding LPCAT, LPAAT, and CPT (Damude pg. 25 para. 297, pg. 32 para. 340). These references do not teach that the recombinant microorganism comprises a gene encoding Cytb5.
Regarding claim 13, Yazawa teaches that polyunsaturated fatty acid desaturation requires cytochrome b5 (Yazawa pg. 2185-6 “Introduction”). Yazawa further teaches overexpression of cytochrome b5 to enhance PUFA production in S. cerevisiae (Yazawa “Abstract”). Yazawa teaches that cytochrome b5 is thought to be an electron donor for fatty acid desaturases to introduce a double bond in fatty acids and that expression of cytochrome b5 enhances fatty acid desaturase activity (Yazawa pg. 2191 “Discussion” para. 2).
It would have been obvious to a skilled artisan, before the effective filing date, to combine the teachings of Scaife, Damude, and Yazawa, resulting in a recombinant Auxenochlorella strain with LPCAT, LPAAT, CPT, and Cytb5 expressed. Damude teaches a recombinant microorganism for PUFA production having LPCAT, LPAAT, and CPT, disclosing that these enzymes are advantageous in PUFA production (Damude pg. 25 para. 293, 297). Yazawa similarly teaches PUFA production in a recombinant microorganism, with the overexpression of Cytb5 being advantageous to this process (Yazawa “Abstract”). It would have been obvious to a skilled artisan that Cytb5 could be additionally incorporated into the strain as taught by Damude and Scaife to enhance PUFA production.
A person of ordinary skill in the art would have been motivated to combine these teachings and additionally incorporate Cytb5 into a recombinant strain because Yazawa teaches that Cytb5 enhances the activity of desaturases, and it would be considered advantageous to express Cytb5 in a recombinant strain comprising desaturases as taught by Scaife and Damude for PUFA production.
A skilled artisan would have a reasonable expectation of success in making this combination to achieve the predictable outcome of enhanced PUFA production in a strain comprising the genes recited in claim 13, given the teachings of Damude and Yazawa that these genes are advantageous in industrial PUFA production.
Response to Arguments
Applicant’s response filed 11/13/2025 has been fully considered, and in light of amendments to the claims, the rejection of claims 1-3 and 6 under 35 U.S.C. § 102 has been withdrawn. However, upon further consideration, new grounds of rejection of claims 1-3 and 7-13 are made under 35 U.S.C. § 103 as set forth above. Given these new grounds of rejection, the arguments presented regarding claims rejected under 35 U.S.C. § 102 are moot.
Responses to pertinent arguments regarding Scaife and Damude are provided below.
Applicant argues that a person of skill in the art would not extrapolate from work in Thraustochytrium to Auxenochlorella protothecoides because Thraustochytrium is a marine stramenopile protist that is phylogenetically and mechanistically distinct from the claimed Auxenochlorella protothecoides, and that this is not merely a difference of host context-it is a fundamental biological incompatibility. Scaife provides disclosure for carrying out engineering in Thraustochytrium but not in Auxenochlorella protothecoides. Applicant additionally argues that a person of skill in the art would not combine the Scaife work in Thraustochytrium with the Damude work in Yarrowia sp. for this same reason.
In response to this argument, it is noted that Scaife teaches methods for the production of PUFAs using microorganisms (col. 25 lines 9-13). Scaife specifically states that “An artisan of ordinary skill, having read the present disclosure and having such reagents in hand, will readily be able to identify appropriate host cells in which such elements are active. Host cells that may be used in the provided methods, compositions and kits include microalgae. Microalgae that
may be used include, but are not limited to … Chlorella protothecoides (Scaife col. 25 lines 45-67, col. 26 line 9). Thus, Scaife teaches that various host cells can be used in the methods for producing PUFAs, and expressly lists Chlorella protothecoides, which is now known as Auxenochlorella protothecoides, as one such host cell that may be used in the methods. Additionally, Scaife teaches that yeast, including Yarrowia sp., can be utilized in the provided methods (Scaife col. 27 lines 1-5). A skilled artisan would therefore recognize that Auxenochlorella/Chlorella protothecoides can be utilized in the methods of Scaife, which involve expression of elongase and desaturase enzymes, because Scaife specifically teaches doing so. A skilled artisan would find it obvious to combine the teachings of Scaife and Damude and utilize the specific elongases and desaturases taught by Damude in Yarrowia, as Scaife teaches that both Auxenochlorella/Chlorella protothecoides and Yarrowia sp. can be utilized as host cells for PUFA production, and it would therefore be obvious to try specific enzymes that were successful in Yarrowia in another microorganism that is exemplified by Scaife for the purpose of producing PUFAs.
Applicant argues that yeast systems taught in Damude are not comparable to Auxenochlorella protothecoides. These yeast systems do not provide a reasonable expectation of success for enzyme functionality in a green algae such as Auxenochlorella protothecoides. The recombinant systems used in Damude (e.g., fungal promoters, codon preferences, transformation strategies) are incompatible with chlorophyte architecture of Auxenochlorella protothecoides. Applicant argues that the inventors tested a wide panel of desaturases and elongases-many derived from fungal sources such as Mortierella-and found that only a limited subset functionally produced LC-PUFAs in Auxenochlorella. Nothing in Scaife and Damude teaches which desaturases and which elongases would be operable in Auxenochlorella protothecoides. Thus, the claimed elongases and desaturases that are operable in Auxenochlorella protothecoides are not obvious from Scaife and Damude.
In response to this argument, it is again noted that Scaife teaches using numerous microalgal and fungal host cells in the provided methods, including Auxenochlorella/Chlorella protothecoides and Yarrowia sp. Further, Scaife teaches that “In general, identified reagents (e.g., regulatory elements, vectors, selectable markers, mutagenic agents, etc.) and methodologies (including, for example, methods of mutagenizing) may be utilized together with any appropriate host cell. An artisan of ordinary skill, having read the present disclosure and having such reagents in hand, will readily be able to identify appropriate host cells in which such elements are active” (Scaife col. 26 lines 42-50). Given the teachings of Scaife specifically listing Auxenochlorella protothecoides and Yarrowia sp. as host cells in a method involving expressing elongases and desaturases, a skilled artisan would have a reasonable expectation of success in utilizing the same enzymes that were expressed in Yarrowia (such as those taught by Damude) in Auxenochlorella protothecoides or a variety of other host cells. Based on the teachings of Scaife one of skill in the art would have been capable of adapting the specific expression mechanisms to a variety of hosts and have the knowledge and tools to make such adaptations. Therefore, a skilled artisan would have found it obvious to try, with a reasonable expectation of success, utilizing the enzymes exemplified in the teachings of Damude in a different host, including Auxenochlorella protothecoides.
Applicant argues that the invention represents a novel industrial platform in green algae producing unique, tunable ratios of LC-PUFAs. This is not taught by Scaife and Damude.
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., producing unique, tunable ratios of LC-PUFAs) 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). Here, the claims are directed to a process wherein Auxenochlorella protothecoides encoding elongases and desaturases is cultured. This process is taught by Scaife and Damude, as discussed above. The claims do not require a specific ratio or amount of PUFAs being produced as a result of the method.
Conclusion
Claims 1-3 and 7-13 are rejected. No claims are 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to EMILY F EIX whose telephone number is (571)270-0808. The examiner can normally be reached M-F 8am-5pm ET.
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/EMILY F EIX/Examiner, Art Unit 1653
/JENNIFER M.H. TICHY/Primary Examiner, Art Unit 1653