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 .
Claim Status
The amended claim set filed on 11 June 2026 is acknowledged. Claims 1-4 are currently pending. Of those, claims 1 and 4 are amended. There are no new claims and no claims are withdrawn. Claims 5-13 are cancelled. Claims 1-4 will be examined on the merits herein.
Response to Amendment
Applicants’ arguments filed on 11 June 2026 are acknowledged. For clarity, in this action, said arguments will be referred to as “Remarks”, and the Non-Final Office Action mailed 11 March 2026 will be referred to as “NFOA”.
Claim Interpretation
Claim 1 has been amended to recite, “wherein the recombinant Sap1 polypeptide and/or recombinant Sap2 polypeptide is tagged and optionally in admixture with an adjuvant.” MPEP 2111.04(I) states: “Claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed, or by claim language that does not limit a claim to a particular structure.” The “optional” limitation is interpreted as not required by the claim and therefore does not limit the scope of the claim.
Rejection(s) Maintained
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim Rejections - 35 USC § 101
Claims 1-2 and 4 remain rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural product without significantly more.
The previous rejection has been amended to reflect the amendments to the claims.
Claim 1 recites, “A composition comprising: (a) a recombinant Surface Attachment Protein 1 (Sap1) polypeptide having the amino acid sequence of SEQ ID NO:1, (b) a recombinant Surface Attachment Protein 2 (Sap2) polypeptide having the amino acid sequence of SEQ ID NO:10, or (c) a combination of (a) and (b), wherein the recombinant Sap1 polypeptide and/or recombinant Sap2 polypeptide is tagged and optionally in admixture with an adjuvant.” The limitation is drawn to a natural product because the scope of Sap1 and Sap2 proteins encompassed by the claim includes proteins which are naturally produced by Burkholderia species, as is described in para. 24 and 27 and Figs. 9-10 of the instant specification. In Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576, 591-94, 106 USPQ2d 1972, 1979-81 (2013; herein “Myriad”), the Supreme Court made clear that not all changes in characteristics will rise to the level of a marked difference, e.g., the incidental changes resulting from isolation of a gene sequence are not enough to make the isolated gene markedly different. In this case, incidental changes in the sequence of a protein obtained from an isolated bacterium without genetic engineering of the protein are not enough to make the claimed protein markedly different. While the claim recites “recombinant” Sap1 and/or Sap2 polypeptides, the specification does not teach that any genetic modifications are made to the natural polypeptides encompassed by SEQ ID NOs: 1 and 10; thus, the “recombinant” Sap1 and/or Sap2 polypeptides are not markedly different from the naturally occurring Sap1 and/or Sap2.
Regarding the limitation “wherein the recombinant Sap1 polypeptide and/or recombinant Sap2 polypeptide is tagged and optionally in admixture with an adjuvant”, it is known in the art that protein tags can naturally be found in and on proteins, such as signal peptides and localization tags, as is taught by Raabe (section 1.1.1, para. 1). Thus, the claimed composition comprising tagged recombinant Sap1 and/or recombinant Sap2 is not markedly different from a naturally occurring Sap1 and/or Sap2 because Sap2 proteins contain a native signal sequence, a type of protein tag. Regarding the adjuvant, it is known in the art that bacterial lipopolysaccharide (LPS) may be used as an adjuvant, as is taught by Arenas (Abstract and pg. 530, left col., para. 3). Morici (US2014/0004178) teaches that Burkholderia produces LPS (para. 88) and that it stimulates the immune response in a B. pseudomallei OMV vaccine (para. 165), i.e., is used as an adjuvant. Thus, the claimed composition comprising Sap1 and/or Sap2 in an admixture with an adjuvant is not markedly different from a naturally occurring Burkholderia expressing Sap1 and/or Sap2 and LPS, because the broadest reasonable interpretation of claim 1 encompasses, for example, cultures of Burkholderia and mixtures of lysed Burkholderia, both of which would comprise Sap1 and or Sap2 and LPS expressed by naturally occurring Burkholderia cells.
Claim 2 recites, “wherein the Sap2 polypeptide further comprises a signal peptide.” The limitation is drawn to a natural product because Sap2 proteins contain a native signal sequence, as is described in para. 28 and 101 of the instant specification. Because the scope of the limitation encompasses signal sequences naturally produced by Burkholderia and naturally part of the Sap2 protein, the Sap2 polypeptide further comprising a signal peptide is not markedly different from the natural Sap2 polypeptide containing a signal peptide.
Claim 4 recites, “A kit for diagnosing a Burkholderia infection comprising a recombinant Surface Attachment Protein immobilized on a substrate, comprising: (a) a recombinant Surface Attachment Protein 1 (Sap1) polypeptide having the amino acid sequence of SEQ ID NO:1, (b) a recombinant Surface Attachment Protein 2 (Sap2) polypeptide having the amino acid sequence of SEQ ID NO:10, or (c) a combination of (a) and (b), wherein the substrate is a glass, plastic, polysaccharide, nylon, or nitrocellulose bead, membrane, or plate.” The limitation “immobilized on a substrate” is drawn to a natural product because the scope of the claim includes a membrane, which is a substrate on which the protein(s) can naturally be found, such as the Burkholderia cell membrane, as evidenced by para. 99 and 101 of the instant specification, which teaches that Sap1 and Sap2 are naturally membrane-bound (i.e., substrate-bound) proteins. Thus, the broadest reasonable interpretation of claim 4 encompasses, for example, whole cell Burkholderia or compositions comprising outer membrane vesicles produced from Burkholderia cell membranes (see, e.g., Morici, Abstract). Because the scope of the claim encompasses the natural phenomenon of Sap1 and/or Sap2 polypeptides bound to a Burkholderia cell membrane, the structure of a Sap1 and/or Sap2 immobilized on a substrate is not markedly different from the natural membrane-bound Sap1 and/or Sap2. While the claim recites “recombinant” Sap1 and/or Sap2 polypeptides, the specification does not teach that any genetic modifications are made to the natural polypeptides encompassed by SEQ ID NOs: 1 and 10; thus, the “recombinant” Sap1 and/or Sap2 polypeptides are not markedly different from the naturally occurring Sap1 and/or Sap2.
This judicial exception is not integrated into a practical application because claims 1-2 and 4 do not recite additional elements that integrate the judicial exception into a practical application.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because claims 1-2 and 4 do not require additional elements other than the natural product(s).
Therefore, claims 1-2 and 4 do not qualify as eligible subject matter. See MPEP 2106.
Response to Arguments
Applicant argues (Remarks, pg. 4-5) that claim 1 has been amended to recite that the recombinant Sap1 and/or Sap2 polypeptide is tagged and claim 4 has been amended to recite that the substrate is glass, plastic, polysaccharide, nitrocellulose bead, membrane, or plate and that the claimed composition and kit are markedly different from a natural product.
This argument has been fully considered but is not persuasive. This argument is not persuasive for the reasons set forth in the amended rejection above and reiterated here: Regarding claim 1, a tagged recombinant Sap1 and/or Sap2 is not markedly different from a naturally occurring Sap1 and/or Sap2 because protein tags are naturally occurring phenomena, such as the signal sequence (i.e., a tag) within the natural Sap2 protein, as is described in para. 28 and 101 of the instant specification. Regarding claim 4, the kit comprising a recombinant Sap1 and/or recombinant Sap2 polypeptide immobilized on a substrate is not markedly different than the natural Sap1 and/or Sap2 polypeptides because the full scope of the claim encompasses membrane-bound Sap1 and/or Sap2, which are naturally found on the Burkholderia cell membrane, as evidenced by para. 99 and 101 of the instant specification.
Claim Rejections - 35 USC § 102
Claims 1-4 remain rejected under 35 U.S.C. 102(a)(1) as being anticipated by Morici (US 2014/0004178 A1; cited in IDS) as evidenced by Hayden et al. (2012, “Burkholderia pseudomallei 1026b chromosome 2, complete sequence”; herein “Hayden”) and Raabe et al. (2019, Biochim. Biophys. Acta; herein “Raabe”).
The previous rejection has been amended to reflect the amendments to the claims.
Regarding claims 1-2, Morici teaches a vaccine comprising B. pseudomallei outer membrane vesicles (OMVs) (para. 245) and an adjuvant (para. 249 and 275). Morici teaches that the OMVs are naturally derived from B. pseudomallei 1026b (para. 171) and comprise the protein BPSS1860 (Table 3), which comprises an amino acid sequence identical to the instant SEQ ID NO: 10 (see Figure 1 for alignment below), as is evidenced by Hayden (pg. 2). The full sequence of BPSS1860 contains an amino acid sequence identical to instant SEQ ID NO: 96 (see Figure 2 for alignment below), as is evidenced by Hayden (pg. 2). This SEQ ID NO: 96 is identified as a signal peptide (i.e., a type of protein tag, as is evidenced by Raabe, section 1.1.1, para. 1) by the instant specification (para. 101). While both Morici and Hayden are silent on the function of this peptide sequence, the function of a “signal peptide” is inherent to its structure; thus, because the structure is present in the amino acid sequence taught by Hayden, it is presumed that the structure has the function of a signal peptide. See MPEP 2112.01(I): “Where the claimed and prior art products are identical or substantially identical in structure or composition,… 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).”
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Figure 1: Alignment of instant SEQ ID NO: 10 (Qy) with Hayden’s B. pseudomallei 1026b protein (Db).
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Figure 2: Alignment of instant SEQ ID NO: 96 (Qy) and residues 1-20 of Hayden’s BPSS1860 protein (Db).
Regarding claim 3, Morici teaches a method comprising administering the OMV vaccine comprising an adjuvant to mice (para. 247), which conferred significant protection against challenge with B pseudomallei (para. 248-249), i.e., immunized the mice against a Burkholderia infection.
Regarding claim 4, Morici teaches that BPSS1860 is an outer membrane/extracellular protein (Table 3), i.e., it is immobilized to the outer membrane, which may act as a substrate. With respect to the limitation in the preamble of claims 4, please note that MPEP 2111.02(II) states "a preamble generally is not limiting when the claim body describes a structurally complete invention such that deletion of the preamble phrase does not affect the structure or steps of the claimed invention." In the instant case, claim 4 is drawn to a product, and the preamble does not affect the structure of the product. The preamble in this case recites a statement of purpose or use, and therefore must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art.
Response to Arguments
Applicant argues (Remarks, pg. 5-6) that Morici and Hayden fail to teach a recombinant Sap2 polypeptide with a tag or immobilization of a recombinant Sap2 polypeptide on a substrate.
This argument has been fully considered but is not persuasive. As written, claims 1 and 4 require the composition or kit to comprise (a) a recombinant Sap1 polypeptide, (b) a recombinant Sap2 polypeptide, or a combination of (a) and (b), i.e., only one of the three alternatives is required. Therefore, in order for Morici to anticipate claim 1, Morici need only teach the recombinant Sap1 polypeptide, the recombinant Sap2 polypeptide, or a combination of both polypeptides. Because Morici teaches a recombinant Sap1 polypeptide having an amino acid sequence identical to SEQ ID NO: 1 and comprising a tag, claim 1 is anticipated. In order for Morici to anticipate claim 4, Morici need only teach the recombinant Sap1 polypeptide immobilized on a substrate, the recombinant Sap2 polypeptide immobilized on a substrate, or a combination of both polypeptides immobilized on a substrate. Because Morici teaches a membrane-bound Sap1 polypeptide (i.e., immobilized on a membrane substrate), claim 4 is anticipated. Hayden is relied upon to provide the full amino acid sequence of the Sap1 polypeptide BPSS1860 taught by Morici, not to teach the immobilization of either Sap1 or Sap2 to a substrate.
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.\
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BAILEY M MORGAN whose telephone number is (703)756-5388. The examiner can normally be reached M-F 9-5 ET.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, SAMIRA JEAN-LOUIS can be reached at (571) 270-3503. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/BAILEY M MORGAN/Examiner, Art Unit 1645
/SAMIRA J JEAN-LOUIS/Supervisory Patent Examiner, Art Unit 1642
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