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
Applicants’ election without traverse of Group II (i.e., claims 12-20 and 33-44 drawn to a recombinant host cell engineered to directly express a plurality of heparosan oligosaccharides) in the reply filed on 03/18/2024 is acknowledged. Additionally, Applicants’ election of Species B (i.e., single and specific heparosan oligosaccharide, based on size or mass; Applicants’ election: dodecasaccharide size); and Species C (i.e., single and specific non-pathogenic bacterial strain indicating: 1. A single and specific order in which the genes of the cluster have been cloned into the non-pathogenic bacterial strain or whether the genes are cloned in any order, Applicants’ election: the genes of the gene cluster have been cloned into the recombinant host cell in the order KfiC, KfiD, KfiA, KfiB; 2. Whether the genes of the cluster have been cloned individually or as a cluster, Applicants’ election: the genes have been cloned as a cluster; 3. A single and specific isoform of elmA, Applicants’ election: isoform elmA-1 and all sequence variations thereof), in the reply filed on 12/06/2024 is acknowledge.
Claims 1-11, 21-31 and 33 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention there being no allowable generic or linking claim; similarly claims 14, 17-18, 33-43 are withdrawn from further consideration pursuant to 1.142(b) as being drawn to a nonelected species there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 03/18/2024.
Status of Claims
Claims 1-44 were originally filed on 10/25/2021.
The amendment received on 12/06/2024, cancelled claims 20, 32, 44; and amended claims 23, 25, 35 and 37.
The amendment received on 12/16/2025, amended claim 12.
Claims 1-19, 21-31, 33-43 are currently pending; and claims 12-13, 15-16 and 19 are under consideration.
Priority
The present application claims the benefit under 35 U.S.C 119 (e) to U.S. Provisional Application No. 62/838,432 filed April 25th 2019. Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C 119 (e) or under 35 U.S.C 120, 121, or 365 (c ) is acknowledged. Additionally, The present application claims status as a 371 (National Stage) of PCT/US2020/029902 filed April 24th 2020.
Response to Arguments
1. Applicants' arguments filed 12/16/2025 regarding the objections to the disclosure, have been fully considered and are persuasive. The objections to the specification have been withdrawn.
2. Applicants' arguments filed 12/16/2025 regarding the 35 U.S.C. 102(a)(1) as being anticipated by Barreteau et al., Carbohydrate Research 360 (2012) pp. 19-24 (herein after “Barreteau”) as evidenced by Sigulinsky et al., Carbohydr Res. (2010), 345(2) pp. 250-256 (herein after “Sigulinsky”), and Zhang et al., Metabolic Engineering, 14(2012) pp. 521-527 (herein after “Zhang”); have been fully considered and are persuasive. The 35 U.S.C. 102(a)(1) rejection of claims 12-13, 16 and 19 has been withdrawn.
3. Applicants' arguments filed 12/16/2025 regarding the 35 U.S.C. 103 as being unpatentable over Barreteau et al., Carbohydrate Research 360 (2012) pp. 19-24 (herein after “Barreteau”), Legoux et al., Journal of Bacteriology (1996) vol. 178, No. 24, pp. 7260-7264 (cited in the IDS filed on 10/21/2021)(herein after “Legoux”), and Zhang et al., Metabolic Engineering, 14(2012) pp. 521-527 (herein after “Zhang”); have been fully considered but are not persuasive. The 35 U.S.C. 103 rejection of claims 12 and 15-16 has been maintained.
New Objections
Claim Objections
Claim 12 is objected to because of the following informalities: spelling. Line 11 recites “oligosacccharides” Appropriate correction is required.
Specification
The disclosure is objected to because of the following informalities: sequence IDs not present in the specification.
Paragraph [0081],of the instant specification makes reference to Table 1, which depicts plasmids and expression plasmids that are 10 or more nucleotides. Pursuant to MPEP 2422.01, Nucleotide and/or amino acid sequences as used in 37 CFR 1.821 through 37 CFR 1.825 are interpreted to mean an unbranched sequence of four or more amino acids or an unbranched sequence of ten or more nucleotides, and thus require a sequence listing. However, plasmids and expression plasmids disclosed in Table 1, at pg. 17 of the specification filed on 12/16/2025 are longer than ten or more nucleotides and do not include sequence identification numbers.
Appropriate correction is required.
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d).
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Examiner’s note: the “marked-up” copy/version of previously-submitted specification, filed on 12/16/2025 does not include the deletions shown with strikethrough or brackets and/or insertions shown with underlining; thus the “marked-up” version and the “clean version” filed on 12/16/2025 appear to be identical. Appropriate correction is required.
New Rejections in Light of Amendments
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.
1. Claim 12 is 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. This is a new matter rejection.
In the instant case, claim 12 was amended to recite: “… wherein the recombinant host cell is engineered to directly express a plurality of heparosan oligosaccharides of a preferred oligosaccharide size profile controllably selected from a possible range of DP4 to DP32 when cultured under predetermined conditions, wherein the predetermined conditions comprise induction time, culture temperature, culture media, and culture time, and wherein the induction time, the culture temperature, the culture media, and the culture time are predetermined to select and control the preferred oligosaccharide size profile of the plurality of heparosan oligosaccharides such that a majority of the plurality of heparosan oligosaccharides range in size from approximately DP4 to approximately DP14.”
Applicants stated in their remarks that “no new matter is added by way of amendments.”(see Remarks, filed 12/16/2025, pg. 11, lines 2 and 9). However, the support (i.e., specification filed 12/16/2025) provided by Applicants does not support that the amendments to claim 12 were previously presented, as the specification is silent about a degree of polymerization (DP) range of DP4 to DP32; additionally there is no mention of the majority of the plurality of heparosan oligosaccharides ranging in size from approximately DP4 to approximately DP14.
The specification is void of evidence that would clearly support the newly added limitations to claim 12. The specification does not teach the specifically claimed oligosaccharide size profile from a possible range of DP4 to DP32, nor that the majority of the plurality of heparosan oligosaccharides range in size from approximately DP4 to approximately DP14. Examination of the instant support, in particular Figs. 29-30E; illustrate results of size-controlled oligosaccharide production in which hexasaccharide and octasaccharide were the major products (see instant specification, pg. 26, para[00113]). Similarly Figs. 32A-32D show characterization of major oligosaccharides: tetra-, hexa-, octa-, and deca-saccharides, after separation through prep-HPLC and confirmation through mass spectrometry (see pg. 26, para[00114]). Additionally, para[00112] at pg. 25 of the instant specification recites that the products revealed the presence of heparosan oligosaccharides of DP4 to DP10 (FIG. 27); and as the digestion progressed, the proportions ofDP6 and DP8 were found to be the highest. Furthermore, para[0070] of the instant specification recites that partial digestion of recombinant heparosan from E. coli BL21-CDAB with heparinase I enzyme for 5 minutes gave a chromatographically well-resolved oligosaccharide profile, ranging from DP2 to DP24, as shown in FIG. 7A (see pg. 11-12 and Fig. 7A). Therefore, positive recitation of oligosaccharides ranging in size from DP2 to DP24, with DP24 being the highest, does not provide support in claiming that the recombinant host cell is engineered to directly express a plurality of heparosan oligosaccharides a preferred oligosaccharide size profile controllably selected from a possible range of DP4 to DP32 and that a majority of the plurality of heparosan oligosaccharides range in size from approximately DP4 to approximately DP14.
The claimed genus encompasses heparosan oligosaccharides of a preferred oligosaccharide size profile controllably selected from a possible range of DP4 to DP32. Pursuant to MPEP 2163.03(V), [a]n original claim may lack written description support when . . . (2) a broad genus claim is presented but the disclosure only describes a narrow species with no evidence that the genus is contemplated. See Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1349-50 (Fed. Cir. 2010) (en banc). "Even if a claim is supported by the specification, the language of the specification, to the extent possible, must describe the claimed invention so that one skilled in the art can recognize what is claimed. The appearance of mere indistinct words in a specification or a claim, even an original claim, does not necessarily satisfy that requirement." Enzo Biochem, Inc. v. Gen-Probe, Inc., 323 F.3d 956, 968, 63 USPQ2d 1609, 1616 (Fed. Cir. 2002). Therefore, the claimed heparosan oligosaccharides of a preferred oligosaccharide range of DP4 to DP32 and the claimed majority of the plurality of heparosan oligosaccharides range in size from approximately DP4 to approximately DP14 is not expressly described.
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.
2. Claim 12 is 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. The claim recites the phrase “preferred oligosaccharide size profile” in lines 5 and 11, which is clearly a preference of the oligosaccharide size profile. Such preference creates confusion over the intended scope of the claim. Pursuant MPEP 2173.05(d) description of examples or preferences is properly set forth in the specification rather than the claims. Therefore the phrase “preferred oligosaccharide size profile” renders the claim indefinite because an ordinary skilled artisan would not be able to ascertain the metes and bounds of the claimed heparosan oligosaccharides based on the preferred size range. Additionally, instant claim 12 recites a narrow range in heparosan oligosaccharides size (i.e., from approximately DP4 to approximately DP14) and a broader range of in heparosan oligosaccharides size (i.e., range of DP4 to DP32), therefore the narrow range fails within the broader range and thus renders the claim indefinite because the metes and bounds of the claimed plurality of heparosan oligosaccharides expressed by the recombinant host cell are not discernible.
Maintained/Modified Rejections
Claim Rejections - 35 USC § 103
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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.
103 - KSR Examples of 'Rationales' Supporting a Conclusion of Obviousness
(Consistent with the "Functional Approach" of Graham)
Further regarding 35 USC 103(a) rejections, the Supreme Court in KSR International Co. v. Teleflex Inc., 550 U.S. 398, 127 S. Ct. 1727, 82 USPQ2d 1385, 1395-97 (2007) (KSR) identified a number of rationales to support a conclusion of obviousness which are consistent with the proper "functional approach" to the determination of obviousness as laid down in Graham. The key to supporting any rejection under 35 U.S.C. 103 is the clear articulation of the reason(s) why the claimed invention would have been obvious. The Supreme Court in KSR noted that the analysis supporting a rejection under 35 U.S.C. 103 should be made explicit.
Exemplary rationales that may support a conclusion of obviousness include:
(A) Combining prior art elements according to known methods to yield predictable results;
(B) Simple substitution of one known element for another to obtain predictable results;
(C) Use of known technique to improve similar devices (methods, or products) in the same way;
(D) Applying a known technique to a known device (method, or product) ready for improvement to yield predictable results;
(E) "Obvious to try" - choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success;
(F) Known work in one field of endeavor may prompt variations of it for use in either the same field or a different one based on design incentives or other market forces if the variations are predictable to one of ordinary skill in the art;
(G) Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention.
Note that the list of rationales provided is not intended to be an all-inclusive list. Other rationales to support a conclusion of obviousness may be relied upon by Office personnel.
Also, a reference is good not only for what it teaches by direct anticipation but also for what one of ordinary skill in the art might reasonably infer from the teachings. (In re Opprecht 12 USPQ 2d 1235, 1236 (Fed Cir. 1989); In re Bode 193 USPQ 12 (CCPA) 1976).
3. Claims 12-13, 15-16 and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Barreteau et al., Carbohydrate Research 360 (2012) pp. 19-24 (herein after “Barreteau”) as evidenced by Sigulinsky et al., Carbohydr Res. (2010), 345(2) pp. 250-256 (herein after “Sigulinsky”), in view of Legoux et al., Journal of Bacteriology (1996) vol. 178, No. 24, pp. 7260-7264 (cited in the IDS filed on 10/21/2021)(herein after “Legoux”), and Zhang et al., Metabolic Engineering, 14(2012) pp. 521-527 (herein after “Zhang”).
Regarding claim 12, Barreteau teaches production of intracellular heparosan and derived oligosaccharides by lyase expression in metabolically engineered E. coli K-12 (see pg. 19, Title), where the cloning and expression of KfiADCB into Escherichia coli K-12 were found sufficient for the production of heparosan (see pg. 19, Abstract). Barreteau adds that production of heparosan-derived oligosaccharides was developed to favor an intracellular degradation of the cytoplasmic polysaccharide which led to the intracellular expression of a heparosan degrading enzyme together with that of the K5 biosynthetic enzymes (see pg. 20, right column, last paragraph). The lyase encoding gene elmA is naturally present in the E. coli K5 genome and the coding sequence was amplified by PCR and cloned in a third low copy expression vector compatible with those expressing the kfiABCD genes (see pg. 20, right column, paragraph 2 and pg. 21, left column, paragraph 1). Barreteau also teaches that the resulting recombinant strain was grown in LB medium at a temperature of 37°C except noted otherwise (see pg. 23, left column, paragraph 3). Barreteau adds that most of the heparosan fraction was kept intracellularly and was composed of various oligosaccharides according to the TLC analysis (see pg. 21, left column, paragraph 1). Barreteau’s Tables 1 and 2, which indicate that the products are oligosaccharides from (degree of polymerization) DP2 to DP10 (see pg. 21, left column, paragraph 1 and Tables 1 and 2).
Additionally, MPEP 2144.05(I) states that "[i]n the case where the claimed ranges "overlap or lie inside ranges discloses by the prior art" a prima facie case of obviousness exists. Therefore, the claimed majority of the plurality of heparosan oligosaccharides range in size from: a) a preferred oligosaccharide size profile controllably selected from a possible range of DP4 to DP32; and b) a majority of heparosan oligosaccharides range in size from approximately DP4 to approximately DP14 would have been obvious to one of ordinary skill in the art since the prior art range (i.e., oligosaccharides from DP2 to DP10) lies within the claimed possible and preferred ranges (i.e., DP4 to DP32 and DP4 to DP14).
With respect to wherein the induction time, the culture temperature, the culture media, and culture media and culture time are predetermined to select and control the preferred oligosaccharide size profile of the plurality of heparosan oligosaccharides such as that a majority of the plurality of heparosan oligosaccharides range in size from approximately DP4 to approximately DP14, as recited in instant claim 12:
Barreteau teaches that production of polysaccharides in high cell density cultures were carried out in 0.5L or 3L reactors containing a mineral culture medium (see pg. 23, right column, paragraph 2). The high-cell density culture consisted of three phases: (i) an exponential-growth phase, which started with inoculation of the bioreactor and lasted until exhaustion of the initially added glucose (17.5 g/L), (ii) a 5-h fed-batch phase with a high substrate feeding rate (glycerol, 2.4 mL h -1) and (iii) a 40-h fed-batch
phase with a lower substrate feeding rate (glycerol, 1.5 mL h -1) (see pg. 23, right column, paragraph 2). Temperature was maintained at 33 °C during the first growth phase and 28 °C for the last two phases (see pg. 23, right column, paragraph 2). Since Barreteau’s Table 1 and Table 2 display DP2 to DP10 oligosaccharides, which fall within the claimed heparosan oligosaccharides ranging in size from approximate DP4 to approximate DP14, it must follow that Barreteau’s culture conditions (i.e., time, temperature and culture media) constitute the claimed predetermined conditions to yield heparosan oligosaccharides ranging in size from approximately DP4 to DP14, as recited in instant claim 12.
Moreover, regarding product-by-process claims, the Federal Circuit has found that "[e]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process." See MPEP 2113 and In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985). Furthermore, the Federal Circuit found that “[b]ecause validity is determined based on the requirements of patentability, a patent is invalid if a product made by the process recited in a product-by-process claim is anticipated by or obvious from prior art products, even if those prior art products are made by different processes.” See MPEP 2113 and Amgen, Inc. v. F. Hoffmann-La Roche Ltd., 580 F.3d 1340, 1370 n 14, 92 USPQ2d 1289, 1312, n 14 (Fed. Cir. 2009).
Therefore, in the instant case, the predetermined conditions (i.e., induction time, the culture temperature, the culture media), do not aid in the patentability of a recombinant host cell of a non-pathogenic bacteria strain having been engineered to comprise the biosynthetic gene cluster KfiA, KfiB, KfiC, KfiD and the gene elmA). All that a prior art reference needs to show is a recombinant host cell comprising the biosynthetic gene cluster KfiA, KfiB, KfiC, KfiD and the gene elmA. Thus, it is not necessary for Barreteau predetermined conditions that comprise induction time, culture temperature, culture media, and culture time, and wherein the induction time, the culture temperature, the culture media, and the culture time are predetermined to select and control the preferred oligosaccharide size profile of the plurality of heparosan oligosaccharides such that the majority of the plurality of heparosan oligosaccharides range in size from approximately DP4 to approximately DP14, as recited in claim 12.
It is sufficient for Barreteau to teach a recombinant host cell of a non-pathogenic bacteria strain having been engineered to comprise the biosynthetic gene cluster KfiA, KfiB, KfiC, KfiD and the gene elmA recited in instant claim 12, which are met and are discussed above. Therefore, the predetermined conditions - induction time, the culture temperature, the culture media- for the selection and control of the preferred oligosaccharide size profile of the plurality of heparosan oligosaccharides such that a majority of the plurality of heparosan oligosaccharides range in size from approximately DP4 to approximately DP14 are not structurally limiting. As such, the teachings of Barreteau satisfy the claim limitations recited in instant claim 12.
Regarding claim 13, Barreteau teaches that the structure of the repeated [GlcAb-4GlcNAca1,4] motif in the K5 polymer was confirmed by NMR analysis (see pg. 20, right column, first paragraph), and that the average molecular weight of the polysaccharide obtained by SEC-MALLS analysis was around 105 kDa (~DP 500) (see pg. 20, right column, paragraph 1). This value was slightly higher than the one reported for the conventional extracellular K5 polysaccharide (50–80 kDa) (see pg. 20, right column, paragraph 1). As such, Barreteau teaches that producing a normal heparosan without expressing the export genes kpsC and kpsS, therefore Barreteau’s results are indicative that the role of the export system is restricted to the control of the size of the polymer (see pg. 20, right column, paragraph 1).
Sigulinsky evidences the preparation of size-defined [15N] N-acetylheparosan oligosaccharides from E. coli-derived [15N]-enriched N-acetylheparosan (see pg. 1, Abstract). Where optimized growth conditions of E. coli in minimal media containing 15NH4Cl yielded [15N] N-acetylheparosan on a preparative scale (see pg. 1, Abstract). Sigulinksky’s Figure 6, shows a comparison between relative abundance of 14N-labeled (i.e., negative control, unlabeled) degree of polymerization 10 (DP10) and degree of polymerization 20 (DP20) N-acetylheparosoan oligosaccharides and 15N-labeled (see pg. 4, paragraph 1). It can be appreciated that the relative abundance of unlabeled DP 10 (Figure 6A) and DP 20 (Figure 6B) is above 50%. Although Sigulinsky does not show evidence of unlabeled DP12 heparosan oligosaccharides, 15N-enriched heparosan oligosaccharides DP 12 were identified (see pg. 14, Table 1 and pg. 12, Figure 5D). As such, it must follow that unlabeled DP12 heparosan oligosaccharides are also generated under optimized growth conditions of E. coli strain K5 grown in minimal media.
Similarly, where the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, a prima facie case of either anticipation or obviousness has been established. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). "When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990). Therefore, the prima facie case can be rebutted by evidence showing that the prior art products do not inherently possess the characteristics of the claimed product. In re Best, 562 F.2d at 1255, 195 USPQ at 433. In the instant case, the teachings of Barreteau read on the claim limitations recited in claim 13, wherein the dodecasaccharide size is the most prevalent size among the plurality of heparosan oligosaccharides because the recombinant cell of Barreteau expresses the kfiABCD genes as well as the elmA gene and produces heparosan DP2-DP10. Therefore, the claimed dodecasaccharide size as being the most prevalent size among the plurality of heparosan oligosaccharides would have been obvious to one skilled in the art.
Regarding claim 15, Barreteau teaches that the lyase encoding gene elmA is naturally present in the E. coli K5 genome (see pg. 20, right column, paragraph 2); and that the coding sequence possesses three alternative possible initiation codons, all leading to active sequences when expressed in E. coli K-12 but only the shortest one being entirely intracellular (see pg. 20, right column, paragraph 2).
However, Barreteau does not expressly teach wherein the gene elmA comprises one of the isoforms elmA-1, elmA-2, or elmA-3 as recited in instant claim 15.
Legoux teaches that the eliminase-encoding gene, designated elmA, has been cloned from E. coli K5 by expression in E. coli K-12 (see pg. 7260, Abstract). The K-12 genome is devoid of the elmA sequence, and the elmA gene product is 820 amino acids long (see pg. 7260, Abstract). Active recombinant eliminase is produced by K-12 cells in both cell-bound and secreted forms (see pg. 7260, Abstract). Legoux teaches that in addition to the triplet that opens the elmA reading frame, there were two in-frame ATG codons, each preceded by a possible Shine-Dalgarno motif; one was located at nucleotide position 1333 and the other was at position 1580 of the long open reading frame (see pg. 7261, left column, last paragraph). Thus, three different constructions, corresponding to three possible starts, were undertaken (see pg. 7261, left column, last paragraph). These fragments were each placed under the control of an IPTG-induced artificial promoter in pEMR466, an expression vector for E. coli, to yield pEMR868, pEMR886, and pEMR869 (see pg. 7261, left column, last paragraph). Interestingly, eliminase activity was found both in the culture medium and in the biomass of RR1 cells transformed by either pEMR868 or pEMR886, whereas the activity could be detected only in the biomass of cells expressing the shortest version (see pg. 7261, right column, paragraph 1). The extracellular eliminase produced by E. coli K5 yields short polymers corresponding to 9 to 10 disaccharide residues as major end products of the N-acetyl-heparosan fragmentation, whereas the cell-bound form tends to depolymerize the substrate to a smaller size (see pg. 7291, right column, paragraph 1). As such, the teachings of Barreteau when combined with the teachings of Legoux are suggestive of the claim limitations as recited in instant claim 15, wherein the gene elmA comprises one of the isoforms elmA-1, elmA-2, or elmA-3.
From the teachings of the references, the Examiner recognizes that it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to engineer Escherichia coli K-12 as taught by Barreteau, to express the shortest version of the elmA codon as one of the isoforms of the elmA gene as taught by Legoux. One of ordinary skill in the art before the effective filing date of the claimed invention would have been motivated to do so because the cloning and expression of KfiADCB in combination with the coding sequence elmA expressed in Escherichia coli was known; because the shortest codon which is entirely intracellular was compatible with the expression vector expressing the KfiABCD genes; and because most of the heparosan fraction was kept intracellularly and was composed of various oligosaccharides. One of ordinary skill in the art before the effective filing date of the claimed invention was made would have had a reasonable expectation of success given that it was known that the co-expression of KfiA, KfiB, KfiC and KfiD with the lyase elmA yield oligosaccharides from (degree of polymerization) DP2 to DP10; and given that it was also known that extracellular eliminase produced by E. coli K5 yields short polymers corresponding to 9 to 10 disaccharide residues as major end products of the N-acetyl-heparosan fragmentation, whereas the cell-bound form tends to depolymerize the substrate to a smaller size. Therefore, engineering Escherichia coli BL21 to express the shortest version of the three elmA constructs would support a recombinant host cell of a non-pathogenic bacterial strain wherein the gene elmA comprises one of the isoforms by constituting some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention pursuant and/or utilizing the "Obvious to try" rationale - choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success pursuant to KSR.
Regarding claim 16, Zhang discloses the metabolic engineering of Escherichia coli BL21 for biosynthesis of heparosan, a bioengineered heparin precursor (see pg. 521, Title). Zhang adds that the metabolic engineering of non-pathogenic E. coli BL21 as a production host (see pg. 521, Abstract). Zhang constructed a recombinant E. coli BL21 as a safer host for heparosan production (see pg. 522, right column, paragraph 2). First the heparosan synthesis genes KfiA, KfiB, KfiC and KfiD from E.coli K5 were cloned and six plasmids pKfiA, pKfiC, pKfiAC, pKfiB, pKfiD and pKfiBD were constructed (see pg. 522, right column, paragraph 2). The six plasmids were respectively transformed into E. coli BL21 and accordingly six recombinant strains (sA, sC, sAC, sABC, sACD and sABCD) were obtained respectively (see pg. 522, right column paragraph 2). Zhang also discloses that the results confirmed that the heparosans from E. coli K5 and the engineered E. coli BL21 strains have identical disaccharide repeating unit with a general structure of [--> 4)-ß-D-GlcA (1--> 4)-α-D-GlcNAc (1--> 4)] (see pg. 525, right column, last paragraph). Zhang also adds that as expected, the highest production of heparosan was reached by the co-expression of KfiA, KfiB, KfiC and KfiD (see pg. 526, right column, paragraph 1).
Additionally, In re Japikse, 181 F.2d 1019, 86 USPQ 70 (CCPA 1950) (Claims to a hydraulic power press which read on the prior art except with regard to the position of the starting switch were held unpatentable because shifting the position of the starting switch would not have modified the operation of the device.); In re Kuhle, 526 F.2d 553, 188 USPQ 7 (CCPA 1975) (the particular placement of a contact in a conductivity measuring device was held to be an obvious matter of design choice). See MPEP 2144.04 (C). As such, the particular order in which the genes of the gene cluster have been cloned into the recombinant host cell does not alter or change the claimed desired result: a non-pathogenic bacterial cell strain comprising the gene cluster KfiC, KfiD, KfiA, KfiB, (i.e., BL21-CDAB).
One of ordinary skill in the art before the effective filing date of the claimed invention would have been motivated with reasonable expectation of success given that it was known that heparosans from E. coli K5 and the engineered E. coli BL21 strains have identical disaccharide repeating unit with a general structure of [--> 4)-ß-D-GlcA (1--> 4)-α-D-GlcNAc (1--> 4)]; given that it was known that the highest production of heparosan was reached by the co-expression of KfiA, KfiB, KfiC and KfiD; given that it was known that eliminase activity was detected in the biomass of cells expressing the shortest version of the construct; and given that it was also known that extracellular eliminase produced by E. coli K5 yields short polymers corresponding to 9 to 10 disaccharide residues as major end products of the N-acetyl-heparosan fragmentation, whereas the cell-bound form tends to depolymerize the substrate to a smaller size. Therefore, engineering Escherichia coli BL21 to express the shortest version of the three elmA constructs would support a recombinant host cell of a non-pathogenic bacterial strain wherein the gene elmA comprises one of the isoforms by constituting some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention pursuant and/or utilizing the "Obvious to try" rationale - choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success pursuant to KSR.
Regarding claim 19, Barreteau teaches the bacterial strains, plasmids and growth conditions (see pg. 23, left column, paragraph 3). The strain DJ which is an E. coli K-12 DH1 derivative was used for heparosan production and the cells were grown in LB medium at a temperature of 37°C except noted otherwise (see pg. 23, left column, paragraph3). MPEP 2144.05(I) states that "[i]n the case where the claimed ranges "overlap or lie inside ranges discloses by the prior art" a prima facie case of obviousness exists. Therefore, the claimed one or more temperatures within a range of approximately 14 degrees Celsius to approximately 40 degrees Celsius would have been obvious to one of ordinary skill in the art since the prior art teaches a temperature of 37°C, which lies within the claimed temperature range.
In light of the foregoing discussion, the Examiner concludes that the subject matter defined by the above claims would have been obvious to one of ordinary skill in the art within the meaning of 35 U.S.C 103. Therefore, the invention as a whole would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, as evidenced by the references discussed above.
Response to Arguments
Applicant's arguments filed 12/16/2025 with respect to the 35 U.S.C 103 rejection, have been fully considered but they are not persuasive.
In response to Applicants argument that Barreteau fails to teach or suggest all the elements of independent claim 2 and that the product profile of Zhang is of much higher molecular weight than normal heparosan produced in E. coli (see Remarks, filed 12/16/2025, pg. 14, first paragraph); it is found unpersuasive.
It is acknowledged that there is not a single reference that teaches and/or suggests every claim limitation recited in independent claim 12 and dependent claims 13, 15-16 and 19. However, Applicants are respectfully reminded that the rejection supra are based on obviousness. Pursuant to MPEP 2142, 35 U.S.C 103 authorizes a rejection where, to meet the claim, it is necessary to modify a single reference or to combine it with one or more other references (emphasis added). Since the rejection is based on obviousness, it is unnecessary for every claim limitation to be taught and/or suggested by a single reference. Additionally, the Examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007).
In the instant case, as discussed above in the 35 U.S.C 103 rejection, Barreteau teaches a nonpathogenic E. coli host cell engineered to express the gene cluster KfiABCD and the gene elmA. Therefore, before the effective filing date of the claimed invention, it was known that a nonpathogenic E. coli cell could be modified to co-express the gene cluster of interest (i.e., KfiA, KfiB, KfiC and KfiD) with the lyase elmA, therefore an ordinary skilled artisan would have been motivated with reasonable expectation of success to combine the teachings of Zhang and Legoux in order to arrive at the claimed invention. Since Zhang teaches that the highest production of heparosan was reached by the co-expression of KfiA, KfiB, KfiC and KfiD in nonpathogenic E.coli cells; and Legoux teaches that the eliminase-encoding gene naturally found in E. coli K5 can be expressed in E. coli K-12 which is devoid of the elmA sequence, and that the eliminase activity was detected in the biomass of the transformed cells. Thus the combine teachings of Zhang and Legoux providing a reasonable expectation of success for an ordinary skill artisan to try co-expressing the gene cluster (i.e., KfiA, KfiB, KfiC and KfiD) with one of the three isoforms of the elmA gene in order to arrive at the claimed invention. Therefore, one of ordinary skill in the art would have been motivated to engineer E. coli K-12 as taught by Barreteau to produce heparosan oligosaccharides with a degree of polymerization ranging in size from DP2 to DP10.
With respect to the claimed predetermined conditions, as discussed in the rejection above, the prior art teaches the claimed recombinant host cell engineered to comprise the biosynthetic gene cluster of interest (i.e., KfiA, KfiB, KfiC, KfiD and the gene elmA). Therefore, since the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, a prima facie case of either anticipation or obviousness has been established. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). "When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990). Therefore, the prima facie case can be rebutted by evidence showing that the prior art products do not inherently possess the characteristics of the claimed product. In re Best, 562 F.2d at 1255, 195 USPQ at 433. Thus, a person of ordinary skill in the art would recognize that a host cell engineered to co-expressed KfiA, KfiB, KfiC, KfiD and the gene elmA would inherently produced heparosan oligosaccharides with a degree of polymerization ranging from approximately DP4 to approximately DP14 or from a possible range of DP4 to DP32 when cultured under predetermined conditions.
Therefore, contrary to Applicant’s argument, the Examiner maintains that a person of ordinary skill in the art would have been motivated with reasonable expectation of success to arrive at the claimed invention after reading the teachings of Barreteau, Legoux and Zhang.
Conclusion
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.
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/CLAUDIA ESPINOSA/ Patent Examiner, Art Unit 1654
/LIANKO G GARYU/ Supervisory Patent Examiner, Art Unit 1654