The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
The amendment filed on 3-23-2026 is acknowledged. Claim 1 has been amended.
Election/Restrictions
In light of the amendment filed on 3-23-2026 the restriction requirement filed on 1-22-2026 is withdrawn. Claims 1-12 are pending and currently under examination.
Information Disclosure Statement
The Information Disclosure Statement filed on 3-20-2024 has been considered. An initialed copy is attached hereto.
It should be noted that the listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Priority
Should applicant desire to obtain the benefit of foreign priority under 35 U.S.C. 119(a)-(d), a certified English translation of the foreign application must be submitted in reply to this action. 37 CFR 41.154(b) and 41.202(e).
Failure to provide a certified translation may result in no benefit being accorded for the non-English application.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, 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 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 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”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 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 statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - Sequences appearing in the specification are not identified by sequence identifiers (i.e., “SEQ ID NO:X” or the like) in accordance with 37 CFR 1.831(c). (see page 9 for example).
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.
Claim Objections
Claim 4 is objected to for utilizing the abbreviation for the genus Pseudomonas without defining it upon its first recitation.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-3 and 5-12 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The instant claims are drawn to the detection of any and all microbes utilizing M13 bait phages comprising at least one peptide or polypeptide or fusion protein specific for recognizing the analyte, said peptide or polypeptide or fusion protein being exposed on the protein pVIII and M13 reporter phages comprising at least one peptide or polypeptide or protein for specific recognition of the analyte fused on the protein pIII, and at least one marker conjugated to the capsid of said second phages M13, said marker being selected from a fluorophore, a chromophore, an electrochemically active species or an electrochemiluminescence. Consequently, the instant claims encompass the use of M13 phages (two types) for the detection of any and all bacterial species, viral species, Archaeal species, fungal species and protists. The claims optionally require:
the microbe is a bacterium (claim 2);
the microbe is a Gram-negative bacterium (claim 3);
the microbe is Pseudomonas aeruginosa (claim 4);
wherein the at least one peptide or polypeptide or fusion protein exposed on the protein pVIII has the sequence SEQ. ID NO: 1 (QRKLAAKLT) (see claim 5);
least one peptide or polypeptide or phage recognition protein of the reporter phage has the sequence SEQ. ID NO: 2 (KLAKLAKKLAKLAK) (claim 6);
the marker is a fluorophore (claim 7);
the marker is CF594 (claim 8);
the M13 bait phages are functionalized on magnetic microspheres (claim 9);
the bound M13 bait phages are separated by magnetic capture (claim 10);
the M13 bait phages are bound to an electrode, a polymer or a silicon-based surface (claim 11); or
the bound M13 bait phages are separated by washing (claim 12).
The specification discloses the use of Dynabeads/bait phage-pVIII and the phage-pIII-CF594 (express the KLAKLAKKLAKLAK peptide) for the detection of Pseudomonas aeruginosa. The use of said M13 phages for the detection of Pseudomonas aeruginosa meet the written description requirements set forth under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph. The instant claims, however, encompass the use of M13 phages (two types) for the detection of any and all bacterial species, viral species, Archaeal species, fungal species and protists. None of these methods meet the written description requirements set forth under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph.
To fulfill the written description requirements set forth under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, the specification must describe at least a substantial number of the members of the claimed genus, or alternatively describe a representative member of the claimed genus, which shares a particularly defining feature common to at least a substantial number of the members of the claimed genus, which would enable the skilled artisan to immediately recognize and distinguish its members from others, so as to reasonably convey to the skilled artisan that Applicant has possession the claimed invention. To adequately describe the genus of detection methods, Applicant must not only adequately describe the specific combination of M13 phages that which are effective in detecting a given microbial species. The specification, with the exception of methods utilizing the Dynabeads/bait phage-pVIII and the phage-pIII-CF594 (express the KLAKLAKKLAKLAK peptide) for the detection of Pseudomonas aeruginosa, does not disclose distinguishing and identifying features of a representative number of members of the genus of M13 phages to which the claims are drawn, such as a correlation between their structure of said phages (i.e. the one peptide or polypeptide or fusion protein specific for recognizing a given microbial species present on the “bait phage” and the one peptide or polypeptide or protein for specific recognition of the analyte fused on the protein pIII present on the “reporter phage”), so that the skilled artisan could immediately envision, or recognize at least a substantial number of members of the claimed genus of detection methods. Aside from the Dynabeads/bait phage-pVIII and the phage-pIII-CF594, the specification is silent with regard to any M13 bait or detection phage that has efficacy in detecting any microbial species. The specification is limited to methods utilizing the Dynabeads/bait phage-pVIII and the phage-pIII-CF594 (express the KLAKLAKKLAKLAK peptide) for the detection of Pseudomonas aeruginosa. Therefore, the specification fails to adequately describe at least a substantial number of members of the genus of M13 phages to which the claims refer.
MPEP § 2163.02 states, “[a]n objective standard for determining compliance with the written description requirement is, 'does the description clearly allow persons of ordinary skill in the art to recognize that he or she invented what is claimed' ”. The courts have decided:
The purpose of the “written description” requirement is broader than to merely explain how to “make and use”; the applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the “written description” inquiry, whatever is now claimed.
See Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Federal Circuit, 1991). Furthermore, the written description provision of 35 USC § 112 is severable from its enablement provision; and adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method for isolating it. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (CAFC 1993) and Amgen Inc. V. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016.
MPEP 2163.02 further states, “[p]ossession may be shown in a variety of ways including description of an actual reduction to practice, or by showing the invention was 'ready for patenting' such as by disclosure of drawings or structural chemical formulas that show that the invention was complete, or by describing distinguishing identifying characteristics sufficient to show that the applicant was in possession of the claimed invention” See, e.g., Pfaff v. Wells Elecs., Inc., 525 U.S. 55, 68, 119 S.Ct. 304, 312, 48 USPQ2d 1641, 1647 (1998); Regents of the Univ. of Cal. v. Eli Lilly, 119 F.3d 1559, 1568, 43 USPQ2d 1398, 1406 (Fed. Cir. 1997); Amgen, Inc. v. Chugai Pharm., 927 F.2d 1200, 1206, 18 USPQ2d 1016, 1021 (Fed. Cir. 1991) (one must define a compound by "whatever characteristics sufficiently distinguish it"). Moreover, because the claims encompass a genus of variant species, an adequate written description of the claimed invention must include sufficient description of at least a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics sufficient to show that Applicant was in possession of the claimed genus. However, factual evidence of an actual reduction to practice has not been disclosed by Applicant in the specification; nor has Applicant shown the invention was “ready for patenting” by disclosure of drawings or structural chemical formulas that show that the invention was complete; nor has Applicant described distinguishing identifying characteristics sufficient to show that Applicant were in possession of the claimed invention at the time the application was filed.
Additionally, MPEP 2163 states:
"A patentee will not be deemed to have invented species sufficient to constitute the genus by virtue of having disclosed a single species when … the evidence indicates ordinary artisans could not predict the operability in the invention of any species other than the one disclosed." In re Curtis, 354 F.3d 1347, 1358, 69 USPQ2d 1274, 1282 (Fed. Cir. 2004)”
And:
For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus. See, e.g., Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. Instead, the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are "representative of the full variety or scope of the genus," or by the establishment of "a reasonable structure-function correlation." Such correlations may be established "by the inventor as described in the specification," or they may be "known in the art at the time of the filing date." See AbbVie, 759 F.3d at 1300-01, 111 USPQ2d 1780, 1790-91 (Fed. Cir. 2014) (Holding that claims to all human antibodies that bind IL-12 with a particular binding affinity rate constant (i.e., koff) were not adequately supported by a specification describing only a single type of human antibody having the claimed features because the disclosed antibody was not representative of other types of antibodies in the claimed genus, as demonstrated by the fact that other disclosed antibodies had different types of heavy and light chains, and shared only a 50% sequence similarity in their variable regions with the disclosed antibodies.).
Recently, describing antibodies by their functions was addressed in the Centocor decision (CENTOCOR ORTHO BIOTECH, INC. v ABBOTT LABORATORIES (Fed Cir, 2010-1144, 2/23/2011)). In said case the court stated”
To satisfy the written description requirement, "the applicant must 'convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention,' and demonstrate that by disclosure in the specification of the patent." Carnegie Mellon Univ. v. Hoffmann-La Roche Inc., 541 F.3d 1115, 1122 (Fed. Cir. 2008) (quoting Vas-Cath Inc. v. Mahurkar, 935 F.2d 1555, 1563-64 (Fed. Cir. 1991)). Assessing such "possession as shown in the disclosure" requires "an objective inquiry into the four corners of the specification." Ariad, 598 F.3d at 1351. Ultimately, "the specification must describe an invention understandable to [a person of ordinary skill in the art] and show that the inventor actually invented the invention claimed." Id. A "mere wish or plan" for obtaining the claimed invention is not adequate written description. Regents of the Univ. of Cal. v. Eli Lilly & Co., 119 F.3d 1559, 1566 (Fed. Cir. 1997).
The court further opined that Centocor's suggestion
that our decision in Noelle and the PTO written description guidelines support the view that fully disclosing the human TNF-α protein provides adequate written description for any antibody that binds to human TNF-α. That suggestion is based on an unduly broad characterization of the guidelines and our precedent.
The court concluded that
While our precedent suggests that written description for certain antibody claims can be satisfied by disclosing a well-characterized antigen, that reasoning applies to disclosure of newly characterized antigens where creation of the claimed antibodies is routine. Claiming antibodies with specific properties, e.g., an antibody that binds to human TNF-α with A2 specificity, can result in a claim that does not meet written description even if the human TNF-α protein is disclosed because antibodies with those properties have not been adequately described.
Therefore, because the art is unpredictable, in accordance with the MPEP, the description of methods utilizing the Dynabeads/bait phage-pVIII and the phage-pIII-CF594 (express the KLAKLAKKLAKLAK peptide) for the detection of Pseudomonas aeruginosa is not deemed representative of the genus of methods of detecting any and all microbes utilizing a combination of M13 phages to which the claims refer. Consequently, the written description provision of 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph are not met.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-12 are rejected under 35 U.S.C. 103 as being unpatentable over Carnazza et al. (2015 XVIII AISEM Annual Conference, pages 1-4 – IDS filed on 3-20-2024) and Mosier-Boss et al., Applied Spectroscopy Vol. 57 No 9, pages 1138-1144 – IDS filed on 3-20-2024).
Carnazza et al. disclose the use of PVIII-M13 bacteriophages covalently to magnetic and latex beads to detect Pseudomonas aeruginosa (see abstract and page 2). Carnazza et al. further disclose that the capture beads/bacteria were recovered with a magnetic separator (see page 2) and were subsequently evaluated via an ELISA utilizing an anti-M13 major coat protein PVIII HRP-monoclonal conjugate (see Results and Discussion section on page 2) or with a fluorophore (see section “E” on page 2).
Carnazza et al. differs from the rejected claims in that they don’t explicitly disclose the use of a fluorescent phage for the detection of the bacteria captured by the magnetic beads.
Mosier-Ross et al. disclose the use of fluorescently labeled phages to detect bacteria (see abstract). Mosier-Ross et al further disclose that fluorescently labeled phages can be used to discriminate and detect bacteria and that phage specificity is determined by the interaction between receptors on the host cell outer membrane and the phage host recognition protein (see page 1143). Finally, Mosier-Boss et al. disclose that fluorescent phages can be highly sensitive and protects the fluorophore from degradation (see page 1143).
It would have been obvious for one skill in the art to utilize the fluorescent phages of Mosier-Boss et al. in the detection methods of Carnazza et al. in order to take advantage of the increased sensitivity and ease of use associated with fluorescent phages.
One would have had a reasonable expectation of success as Mosier-Boss et al. disclose that their methods are based on the interaction between receptors on the host cell outer membrane and the phage host recognition protein.
With regard to the specific use of CF594 as the fluorophore and M13 phages as the detection phage, their use is deemed to be an obvious of the method arising from the cited references. The KSR decision sets forth “if a technique has been used to improve one device, and a person of skill in the art would recognize that it would improve similar devices in the same way, using the technique is obvious unless its actual application is beyond that person’s skill”. Given that Mosier-Ross disclose the use of fluorescently labeled phages to detect bacteria and the use of M13 phages and the use of various fluorophores (including CF594) are well established in the art, the use of use of M13 phages and CF594 is well within the capabilities of one of ordinary skill in the art. Hence, the requirements of obviousness under the KSR decision are met.
Claims 1-12 are rejected under 35 U.S.C. 103 as being unpatentable over De Plano et al. (Journal of Immunological Methods Vol. 465, pages 45-52 – IDS filed on 3-20-2024) and Mosier-Boss et al., Applied Spectroscopy Vol. 57 No 9, pages 1138-1144 – IDS filed on 3-20-2024).
De Plano et al. disclose the use of M13 bacteriophages fused to pVIII and covalently to magnetic and latex beads to detect Pseudomonas aeruginosa (see abstract and section 2.2 on page 46). De Plano et al. further disclose that the capture beads/bacteria were recovered with a magnetic separator (see section 2.5 on page 47) and were subsequently evaluated via Raman spectroscopy (see section 2.6 on page 47).
De Plano et al. differs from the rejected claims in that they don’t explicitly disclose the use of a fluorescent phage for the detection of the bacteria captured by the magnetic beads.
Mosier-Ross et al. disclose the use of fluorescently labeled phages to detect bacteria (see abstract). Mosier-Ross et al further disclose that fluorescently labeled phages can be used to discriminate and detect bacteria and that phage specificity is determined by the interaction between receptors on the host cell outer membrane and the phage host recognition protein (see page 1143). Finally, Mosier-Boss et al. disclose that fluorescent phages can be highly sensitive and protects the fluorophore from degradation (see page 1143).
It would have been obvious for one skill in the art to utilize the fluorescent phages of Mosier-Boss et al. in the detection methods of De Plano et al. in order to take advantage of the increased sensitivity and ease of use associated with fluorescent phages.
One would have had a reasonable expectation of success as Mosier-Boss et al. disclose that their methods are based on the interaction between receptors on the host cell outer membrane and the phage host recognition protein.
With regard to the specific use of CF594 as the fluorophore, its use is deemed to be an obvious of the method arising from the cited references. The KSR decision sets forth “if a technique has been used to improve one device, and a person of skill in the art would recognize that it would improve similar devices in the same way, using the technique is obvious unless its actual application is beyond that person’s skill”. Given that Mosier-Ross disclose the use of fluorescently labeled phages to detect bacteria and the use various fluorophores (including CF594) is well established in the art, the use of use of M13 phages and CF594 is well within the capabilities of one of ordinary skill in the art. Hence, the requirements of obviousness under the KSR decision are met.
Claims 1-12 are rejected under 35 U.S.C. 103 as being unpatentable over Rizzo et al. (Sensors & Actuators: B. Chemical, Vol. 329, pages 1-9 – IDS filed on 3-20-2024) and Mosier-Boss et al., Applied Spectroscopy Vol. 57 No 9, pages 1138-1144 – IDS filed on 3-20-2024).
Rizzo et al. disclose the use of M13-pVIII-9aa bacteriophages covalently to magnetic and latex beads to detect Pseudomonas aeruginosa (see abstract and section 2.3 on page 3). Rizzo et al. further disclose that the 9aa peptide has the sequence QRKLAAKLT (see section 2.3 on page 3) the capture beads/bacteria washed and recovered with a magnetic separator (see section 2.4 on page 3) and were subsequently evaluated PCR.
Rizzo et al. differs from the rejected claims in that they don’t explicitly disclose the use of a fluorescent phage for the detection of the bacteria captured by the magnetic beads.
Mosier-Ross et al. disclose the use of fluorescently labeled phages to detect bacteria (see abstract). Mosier-Ross et al further disclose that fluorescently labeled phages can be used to discriminate and detect bacteria and that phage specificity is determined by the interaction between receptors on the host cell outer membrane and the phage host recognition protein (see page 1143). Finally, Mosier-Boss et al. disclose that fluorescent phages can be highly sensitive and protects the fluorophore from degradation (see page 1143).
It would have been obvious for one skill in the art to utilize the fluorescent phages of Mosier-Boss et al. in the detection methods of Rizzo et al. in order to take advantage of the increased sensitivity and ease of use associated with fluorescent phages.
One would have had a reasonable expectation of success as Mosier-Boss et al. disclose that their methods are based on the interaction between receptors on the host cell outer membrane and the phage host recognition protein.
With regard to the specific use of CF594 as the fluorophore, its use is deemed to be an obvious of the method arising from the cited references. The KSR decision sets forth “if a technique has been used to improve one device, and a person of skill in the art would recognize that it would improve similar devices in the same way, using the technique is obvious unless its actual application is beyond that person’s skill”. Given that Mosier-Ross disclose the use of fluorescently labeled phages to detect bacteria and the use various fluorophores (including CF594) is well established in the art, the use of use of M13 phages and CF594 is well within the capabilities of one of ordinary skill in the art. Hence, the requirements of obviousness under the KSR decision are met.
Conclusion
No claim is allowed.
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/ROBERT A ZEMAN/Primary Examiner, Art Unit 1645 June 11, 2026
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