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 .
Election/Restrictions
Applicant’s election without traverse of Group II (claims 1-4, 6-8, 10, 11, 12 and 21) and species of bola glycolipid with acetylation degree of 4, sble (claim 11) and Starmerella bombicola in the reply filed on 08/17/2026 is acknowledged.
Claims 5, 9, and 13-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected Group or Invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 08/17/2026.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 4 and 6 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 4 recites the limitation "said bola sophorolipids" in line 1. There is insufficient antecedent basis for this limitation in the claim. There is no literal nor reasonable inherent antecedent basis for "said bola sophorolipids" is claims 1 or 4. Recitation in claim 1 of bola amphiphilic glycolipids is not a sufficient antecedent basis since such amphiphilic glycolipids includes glycolipids that are not sophorolipids. .” As such, it is not clear as to what claim element “said bola sophorolipids” references such that an ordinarily skilled artisan cannot determine how to avoid infringement.
Claim 6 recites the limitation "the SL biosynthetic cluster" in line 3. There is insufficient antecedent basis for this limitation in the claim. There is no literal nor reasonable inherent antecedent basis for "the SL biosynthetic cluster" wherein a generic recitation of a modified yeast strain in claim 1 does not provide for an antecedent basis for a specific "the SL biosynthetic cluster.” As such, it is not clear as to what claim element “the SL biosynthetic cluster” references such that an ordinarily skilled artisan cannot determine how to avoid infringement.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1, 3, 6, and 12 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Van Bogaert et al. (Synthesis of Bolaform Biosurfactants by an Engineered Starmerella bombicola Yeast, Biotechnol. Bioeng. 113, 2016, 2644-51) (see IDS) as evidenced by GenBank, Accession No. HQ670751.1, 2012, www.ncbi.nlm.nih.gov, and GenBank, Accession No. KC121031, 2013, www.ncbi.nlm.nih.gov.
Van Bogaert, abstract, sets forth:
Bola-amphiphilic surfactants are molecules with
fascinating properties. Their unique configuration consisting of a
long hydrophobic spacer connecting two hydrophilic entities
renders the molecule more water soluble than the average
surfactant, but still allows formation of supramolecular structures.
These properties make them extremely suitable for applications in
in nanotechnology, electronics, and gene and drug delivery. In
general, these compounds are obtained by chemical synthesis. We
report here an efficient microbial production process for the fully
green synthesis of bolaform surfactants. A sophorolipid-producing
Starmerella bombicola yeast strain was disabled in its sophorolipid
acetyltransferase and lactone esterase, which should logically result
in synthesis of non-acetylated acidic sophorolipids; molecules with
the classic amphiphilic structure. Surprisingly, also bolaform
glycolipids were obtained, with an additional sophorose linked to
the free carboxyl end of the acidic sophorolipids as confirmed by MS
and NMR analysis. The obtained titers of 27.7 g/L total product are
comparable to wild type values, and the novel molecules account for
at least 74% of this. Bola-amphiphile biosynthesis proved to be
attributed to the promiscuous activity of both UDP-glucosyltransferases
UGTA1 and UGTB1 from the core sophorolipid pathway,
displaying activity toward non-acetylated intermediates. The
absence of acetyl groups seems to trigger formation of bolaform
compounds starting from acidic sophorolipids. Hence, wild type
S. bombicola produces these compounds only at marginal amounts
in general not reaching detection limits. We created a strain
knocked-out in its sophorolipid acetyltransferase and lactone
esterase able to produce these novel compounds in economical
relevant amounts, opening doors for the application of biological derived
bolaform structures
Regarding claims 1, 3, and 12, the above is a description of a method of producing bola amphiphilic glycolipids, said method comprising culturing a modified Starmerella bombicola yeast strain that comprises a non-functional or dysfunctional Starmerella bombicola lactone esterase (Sble), and/or does not comprise a functional sble gene compared to a non-modified yeast to produce bola amphiphilic glycolipids.
Regarding claim 6, as set forth above, Van Bogaert (abstract) describes “Starmerella bombicola yeast strain was disabled in its sophorolipid acetyltransferase and lactone esterase.” “A S. bombicola strain knocked-out in the lactone esterase gene (sble, GenBank accession number KC121031) and a strain knockedout in the sophorolipid acetyltransferase gene (at, GenBank accession numbers HQ670751).” Van Bogaert, page 2646, left col. GenBank HQ670751 (positions 43-822) evidences that the sophorolipid acetyltransferase gene described by Van Bogaert is identical to SEQ ID NO: 3 of the specification and is therefore an acetyl transferase enzyme 1 (At1) gene as recited in claim 6. Further, GenBank KC121031 (positions 1023-1233) evidences that the lactone esterase gene described by Van Bogaert is identical to SEQ ID NO: 1 of the specification described as a Starmerella bombicola lactone esterase (Sble) gene. “The presence of a free carboxylic group alone, as for products of the single lactone esterase knock-out, does not trigger formation of bolaform sophorolipids; apparently also acetylation needs to be absent.” Van Bogaert, page 2649, right col. Fig. 2 of Van Bogaert shows Bolaform sophorolipids without acetylation. As such, Van Bogaert reports “wherein said bola amphiphilic glycolipids have an acetylation degree of 0.”
Claim(s) 1, 2, 3, 4, 6, and 12 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Van Bogaert et al. (Synthesis of Bolaform Biosurfactants by an Engineered Starmerella bombicola Yeast, Biotechnol. Bioeng. 113, 2016, 2644) (see IDS) as evidenced by GenBank, Accession No. HQ670751.1, 2012, www.ncbi.nlm.nih.gov, and GenBank, Accession No. KC121031, 2013, www.ncbi.nlm.nih.gov, and Roelants et al. (Bubbling insights: unveiling the true sophorolipid biosynthetic pathway by Starmerella bombicola, Biotechnol. Biofuels Bioproducts, 17, 2024, 113).
Van Bogaert, abstract, sets forth:
Bola-amphiphilic surfactants are molecules with
fascinating properties. Their unique configuration consisting of a
long hydrophobic spacer connecting two hydrophilic entities
renders the molecule more water soluble than the average
surfactant, but still allows formation of supramolecular structures.
These properties make them extremely suitable for applications in
in nanotechnology, electronics, and gene and drug delivery. In
general, these compounds are obtained by chemical synthesis. We
report here an efficient microbial production process for the fully
green synthesis of bolaform surfactants. A sophorolipid-producing
Starmerella bombicola yeast strain was disabled in its sophorolipid
acetyltransferase and lactone esterase, which should logically result
in synthesis of non-acetylated acidic sophorolipids; molecules with
the classic amphiphilic structure. Surprisingly, also bolaform
glycolipids were obtained, with an additional sophorose linked to
the free carboxyl end of the acidic sophorolipids as confirmed by MS
and NMR analysis. The obtained titers of 27.7 g/L total product are
comparable to wild type values, and the novel molecules account for
at least 74% of this. Bola-amphiphile biosynthesis proved to be
attributed to the promiscuous activity of both UDP-glucosyltransferases
UGTA1 and UGTB1 from the core sophorolipid pathway,
displaying activity toward non-acetylated intermediates. The
absence of acetyl groups seems to trigger formation of bolaform
compounds starting from acidic sophorolipids. Hence, wild type
S. bombicola produces these compounds only at marginal amounts
in general not reaching detection limits. We created a strain
knocked-out in its sophorolipid acetyltransferase and lactone
esterase able to produce these novel compounds in economical
relevant amounts, opening doors for the application of biological derived
bolaform structures.
Regarding claims 1, 3, and 12, the above is a description of a method of producing bola amphiphilic glycolipids, said method comprising culturing a modified Starmerella bombicola yeast strain that comprises a non-functional or dysfunctional Starmerella bombicola lactone esterase (Sble), and/or does not comprise a functional sble gene compared to a non-modified yeast to produce bola amphiphilic glycolipids. SEQ ID NO: 3 is described in the specification as the gene for acetyl transferase enzyme 1 (At1).
Regarding claim 6, as set forth above, Van Bogaert (abstract) describes “Starmerella bombicola yeast strain was disabled in its sophorolipid acetyltransferase and lactone esterase.” “A S. bombicola strain knocked-out in the lactone esterase gene (sble, GenBank accession number KC121031) and a strain knockedout in the sophorolipid acetyltransferase gene (at, GenBank accession numbers HQ670751).” Van Bogaert, page 2646, left col. GenBank HQ670751 (positions 43-822) evidences that the sophorolipid acetyltransferase gene described by Van Bogaert is identical to SEQ ID NO: 3 of the specification and is therefore an acetyl transfease enzyme 1 (At1) gene as recited in claim 6. Further, GenBank KC121031 (positions 1023-1233) evidences that the lactone esterase gene described by Van Bogaert is identical to SEQ ID NO: 1 of the specification described as a Starmerella bombicola lactone esterase (Sble) gene.
Regarding claims 2 and 4,Van Bogaert further reports a S. bombicola strain having deletion of only the sophorolipid acetyltransferase gene, as shown in Table 1 of Van Bogaert, that also produces bola sophorolipid:
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Roelants, abstract, explains: Recently, Starmerella bombicola strains developed and evaluated in the past were reevaluated unveiling unexpected findings. The AT enzyme encoded in the sophorolipid biosynthetic gene cluster is the only described enzyme known to acetylate sophorolipids, while the SBLE enzyme encoded by the SBLE gene is described to catalyze the conversion of (acetylated) acidic sophorolipids into lactonic sophorolipids. A double knockout of both genes was described to result in the generation of bolaform sophorolipids. However, new experiments performed with respective S. bombicola strains Δsble, Δat Δsble, and Δat revealed inconsistencies with the current understanding of the SL pathway. It was observed that the Δsble strain produces mainly bolaform sophorolipids with higher acetylation degrees instead of acidic sophorolipids.
Roelants, page 5, right col.:
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Reference 14 or Roelants of is Van Bogaert. As such, Roelants evidences that the S. bombicola [Symbol font/0x44]sble strain described by Van Bogaert inherently produces “(acetylated) bola SLs up to an acetylation degree of four in the samples from [Symbol font/0x44]sble strain.”
Further, the specification, page 26, evidences:
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Van Bogaert et a. (2016) referenced by the specification is the same Van Bogaert et al. reference cited for anticipation.
"[T]he discovery of a previously unappreciated property of a prior art composition, or of a scientific explanation for the prior art’s functioning, does not render the old composition patentably new to the discoverer." MPEP 2112(I). “There is no requirement that a person of ordinary skill in the art would have recognized the inherent disclosure at the relevant time, but only that the subject matter is in fact inherent in the prior art reference.” MPEP 2112(II). “In certain circumstances, references cited to show a universal fact need not be available as prior art before the effective filing date of applicant’s claimed invention. In re Wilson, 311 F.2d 266, 135 USPQ 442 (CCPA 1962). Such facts include the characteristics and properties of a material or a scientific truism.” MPEP 2124.
Here, Roelants (and the specification) states that previous described S. bombicola [Symbol font/0x44]sble strains when cultured produces “(acetylated) bola SLs up to an acetylation degree of four in the samples from [Symbol font/0x44]sble strain,” where the same was not recognized by Van Bogaert and by other art due to shortcomings in analytical techniques (detection range of MS analysis) and extraction methods previously employed. That is, the production of bola sophorolipids with acetylation degree up to 4 was inherently present in the prior-described [Symbol font/0x44]sble strain (including in Van Bogaert et al.), but was not recognized due to shortcomings in extraction and analytical techniques. Further, the specification, page 26, directly states and evidences that the S. bombicola [Symbol font/0x44]sble strains reported in Van Bogaert “produces mainly bola SLs with higher acetylation degrees (diAc, triAc and tetraAc).” As such, the evidence of record supports that the S. bombicola [Symbol font/0x44]sble strain described by Van Bogaert when cultured inherently produces bola sophorolipids including at least some acetylated bola sophorolipids with an acetylation degree of up to 4 as recited in claims 2 and 4.
Claim(s) 1, 3, 6, and 12 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Soetaert et al. (U.S. 2016/0168612 A1) as evidenced by GenBank, Accession No. HQ670751.1, 2012, www.ncbi.nlm.nih.gov, and GenBank, Accession No. KC121031, 2013, www.ncbi.nlm.nih.gov.
Soetaert et al., abstract, states:
This disclosure relates to the field of the microbial production of specific types of glycolipids that are potentially useful as replacements for petroleum-based detergents and emulsifiers. This disclosure, more specifically, discloses the usage of yeasts having a dysfunctional acetyltransferase for producing high amounts of bolaamphiphilic glycolipids when using conventional and cheap substrates. Furthermore, the disclosure relates to yeasts having a dysfunctional acetyltransferase optionally combined with a dysfunctional lactonase and/or second glucosyltransferase. The latter microorganisms are capable of producing high amounts of bolaamphiphilic sophorolipids.
Soetaert, in the claims, states:
31. A method of producing symmetric bolaamphiphilic glycolipids having a hydrophobic spacer with hydrophilic glucose molecules at both ends of the spacer, wherein the hydrophilic glucose molecules are linked to both sides of the spacer by a glycosidic bond, the method comprising:
culturing a fungal strain selected from the group consisting of Starmerella (Candida) bombicola, Candida apicola, Candida batistae, Candida floricola, Candida riodocensis, Candida stellate, Candida kuoi, Candida sp. NRRL Y-27208, Rhodotorula bogoriensis sp., Wickerhamiella domericqiae and a sophorolipid-producing strain of the Starmerella clade, wherein the fungal strain comprises:
a dysfunctional acetyltransferase,
a dysfunctional acetyltransferase and a dysfunctional lactonase, or
a dysfunctional acetyltransferase and a dysfunctional cytochrome P450 monooxygenase, or
a dysfunctional acetyltransferase, a dysfunctional lactonase, and a dysfunctional cytochrome P450 monooxygenase,
utilizing fatty alcohols and/or diols as a substrate in order to obtain a fermentation broth comprising a mixture of several types of glycolipids, and
recovering the symmetric bolaamphiphilic glycolipids from the fermentation broth.
“More surprisingly, this disclosure further demonstrates that the total production of glycolipids and the relative amount of the bolaform sophorolipids can be even further increased by using a yeast strain (such as a Starmerella bombicola strain) that is not solely knocked-out in the acetyltransferase gene as described above, but is also knocked-out in the lactonase gene. This double knock-out strain (i.e., ΔatΔlac) is surprisingly performing better than the single acetyltransferase knock-out strain (Δat). In sharp contrast, a strain with a single knock out of this lactonase (Δlac) is not producing these types of molecules (see Table 1). The lactonase gene is described in detail in . . . and the nucleotide and amino acid sequence can be consulted under GenBank accession number KC 121031.” Soetaert, para. [0049].
“A S. bombicola strain knocked-out in the acetyltransferase gene responsible for acetylation of sophorolipids (GenBank accession number HQ670751) was derived from the parental Starmerella bombicola ATCC 22214 strain as described in . . . and is referred to as Starmerella bombicola AT3. For sophorolipid production, the medium described by . . . was used. 37.5 g/L rapeseed oil was added two days after inoculation. Yeast cultures were incubated at 30° C. and 200 rpm for a total time of 10 days.” Soetaert, para. [0087].
“A strain, both knock-out in the acetyltransferase (GenBank accession number HQ670751) and lactonase gene, was created.” Soetaert, para. [0096].
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Regarding claims 1, 3, and 12, the above is a description of a method of producing bola amphiphilic glycolipids, said method comprising culturing a modified Starmerella bombicola yeast strain that comprises a non-functional or dysfunctional Starmerella bombicola lactone esterase (Sble), and/or does not comprise a functional sble gene compared to a non-modified yeast to produce bola amphiphilic glycolipids. SEQ ID NO: 3 is described in the specification as the gene for acetyl transferase enzyme 1 (At1).
Regarding claim 6, GenBank HQ670751 (positions 43-822) evidences that the sophorolipid acetyltransferase gene described by Soetaert is identical to SEQ ID NO: 3 of the specification and is therefore an acetyl transfease enzyme 1 (At1) gene as recited in claim 6. Further, GenBank KC121031 (positions 1023-1233) evidences that the lactone esterase gene described by Soetaert is identical to SEQ ID NO: 1 of the specification described as a Starmerella bombicola lactone esterase (Sble) gene. Fig. 2 of Soetaert shows bolaform sophorolipid lacking any acetylation such that “wherein said bola amphiphilic glycolipids have an acetylation degree of 0.”
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 3, 6, and 12 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of U.S. Patent No. 9,650,658 B2 in view of Soetaert et al. (U.S. 2016/0168612 A1), GenBank, Accession No. HQ670751.1, 2012, www.ncbi.nlm.nih.gov, and GenBank, Accession No. KC121031, 2013.
U.S. Patent No. 9,650,658 B2 is previously published as Soetaert et al. (U.S. 2016/0168612 A1).
The rejections above under 35 U.S.C. 102 in view of Soetaert stated above are incorporated herein by reference.
The patented claims state:
1. A method of producing bolaamphiphilic glycolipids having a hydrophobic spacer with hydrophilic glucose molecules at both ends of the spacer, the method comprising:
growing a yeast strain that comprises a dysfunctional acetyltransferase and a dysfunctional lactonase in a fermentation broth, and
recovering bolaamphiphilic glycolipids produced by the yeast strain from the fermentation broth,
wherein the yeast strain is Starmerella bombicola ATCC 22214, and
wherein the dysfunctional acetyltransferase is produced by:
mutating a gene in the yeast strain encoding the acetyltransferase and the lactonase,
silencing transcription or translation of a gene in the yeast strain encoding the acetyltransferase and the lactonase, and/or
disrupting the function of the acetyltransferase and the lactonase in the yeast strain, and
wherein the total amount of the bolaamphiphilic glycolipids produced is at least 10% of the total amount of several types of glycolipids produced.
4. The method according to claim 3, wherein the yeast strain further comprises:
a dysfunctional glucosyltransferase that is responsible for the second glucosylation step in the sophorolipid biosynthetic pathway.
10. The method according to claim 4, wherein the yeast strain comprises:
a dysfunctional acetyltransferase and a dysfunctional lactonase, and
wherein the bolaamphiphilic glycolipids are non-acetylated, bolaamphiphilic glycolipids consisting of four (4) glucose molecules.
The patented claims directly anticipate at least claims 1, 3, 6, and 12. As discussed, the disrupted acetyltransferase and lactonase as recited in the patented claims is a non-functional at1 gene from a SL biosynthetic cluster and at1 acetyl transferase enzyme gene as evidenced by Soetaert et al. (U.S. 2016/0168612 A1) and cited GenBank entries.
Allowable Subject Matter
Claims 7, 8, 10, 11 and 21 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:
The closest prior art is represented by Roelants et al. as discussed above teaching R. bombicola disabled in its sophorolipid acetyltransferase and lactone esterase. As discussed above, the disabled acetyltransferase gene is associated with SEQ ID NO: 3 associated with SEQ ID NO: 3 of the specification. Claims 7, 8 and 10 require deletion or non-functional At2 and/or At3. At2 is associated with SEQ ID NOS: 5 (nt) and 6 (aa) and At3 is associated with SEQ ID NOS: 7 (nt) and 8 (aa) in the specification.
Roelants, page 7, left col., reports: “As the acetyltransferase from the SL biosynthetic gene cluster was fully removed in the novel Δat_full strain and acetylated compounds were still observed, this indicates the activity of (an)other unknown acetyltransferases active on SLs.” The At2 and At3 genes reported in the specification appear to be the identification of “other unknown acetyltransferases” that do not appear to be reported in the prior art as relevant for acetylation of sophorolipids.
Conclusion
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/TODD M EPSTEIN/Primary Examiner, Art Unit 1652
