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 .
DETAILED ACTION
Election/Restrictions
Applicant’s election without traverse of species in the reply filed on 03/26/2026 is acknowledged.
Group I: Elect one target microorganism from Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli and Staphylococcus epidermidis (claims 9, 13,14).
- Applicant elects Staphylococcus epidermidis as the target
microorganism (readable on claims 1-16) without traverse.
Group II: For peptide (3), elect one peptide sequence from SEQ ID NO.1, SEQ ID NO.2, SEQ ID NO.3 and SEQ ID NO.4 (claims 10, 15, 16).
- Applicant elects SEQ ID NO: 4 as the peptide sequence (readable on
claims 1-16) without traverse.
Group III: Elect one for marker (5) and one for marker (13)
- Marker (5) (method according to claims 2 and 3)
-Applicant elects electrochemical marker for marker (5) (readable on claims 2, 3, 5-7, 11-16) without traverse.
- Applicant elects the single marker of ferrocene for the single marker (readable on claims 2, 3, 5-7, 11-16) without traverse.
- Marker (13) (method according to claim 1)
- Applicant elects semiconductor nanoparticles for marker (13)
(readable on claims 1, 4, 8-10) without traverse.
Claims 1-16 are under consideration.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 09/01/2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code on page 16. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Objections
Claims 1-16 are objected to because of the following informalities:
Claims 1-16: For improved form, remove all numbers in parentheses within the claims that correspond to the drawings. For example from claim 1, (2), (1), etc.
Claims 1-10: Delete the hyphen after the claim numbers (e.g., 1.-).
Claims 4-16: Add a “The” before “method” at the start of the sentence. For example, The method according to claim 1”.
Claim 1: Change “release said marker” to “releases said marker”. Also, change “marker (14) in deactivated form” to “marker in deactivated form (14)” and “marker (14’) in activated form” to “marker in activated form (14’)”.
Claim 2: Add an “A” before “method” at the start of the sentence. For example, “A method for determining…”.
Claim 3: Add an “A” before “method” at the start of the sentence. For example, “A method for determining…”. Change “marked” (lines 8, 9, 10, 11) to “marker”. Change “microorganism-marked phage complex (7) to “microorganism-phage-marker complex” (see 112b below). The “phage-marker complex” is consistent with the first step of “contacting”.
Claim 4: Spell out the acronym “SeC”.
Claims 6-16: Change “characterized in that” to wherein.
Claims 8-10: Add a comma after claim 1 in the preamble.
Claims 9, 13, 14: “Staphilococcus epidermidis” to “Staphylococcus epidermidis”
Claims 10, 15, 16: Change “e” to “and”. Also change “No.” to “NO:”
Claim 12: Add a comma after claim 2.
Claim 13: Add a comma after claim 2.
Claim 14: Add a comma after claim 3.
Claim 15: Add a comma after claim 2.
Claim 16: Add a comma after claim 3.
Appropriate correction is required.
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 1, 3, 4, 7-11, 14, and 16 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 1: The phrase “so that said microorganism (2) reaches said fixation zone (12) to form a phage-target microorganism complex (15) and release[s] said marker (14’) in activated form” is unclear. It is unclear if the microorganism itself plays a role, in the release of the marker bound to the phage, or if the phage releases the marker when binding to the microorganism, or if the marker is released prior to the phage-target microorganism complex forming. It is also unclear how exactly the marker changes from a deactivated form into an activated form, particularly when several options of markers are provided in dependent claims.
Claim 3: Claim 3 recites “letting said phage (4) react with said biological sample (1) so as to allow, if said microorganism (2) is present, the binding of said phage (4) to said microorganism (2) to obtain a sample comprising a microorganism-marked phage complex (7). It is unclear, if during this process, the microorganism itself becomes marked with a marker (e.g., a transfer of the marker) or if microorganism is simply binding to the phage with the marker. For the review, the claim is being interpreted as the marker being retained on the phage.
Claim 4: Claim 4 recites the limitation “wherein said marker (13)…". There is insufficient antecedent basis for this limitation in the claim. Claim 1 only has a marker (14) in a deactivated form or a marker (14’) in an activated form.
Claims 4 and 7: Claim 4 recites “such as SeC”. Claim 7 recites “such as ferrocene”. The language, “such as” is considered exemplary language. Description of examples or preferences is properly set forth in the specification rather than the claims. If stated in the claims, examples and preferences may lead to confusion over the intended scope of a claim, e.g., whether the claimed narrower range is a limitation (See MPEP 2173.05(d) Exemplary Claim Language).
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.
Claims 2, 5-6, 12, 13 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Rees (WO2006105504A1)(cited on IDS, 09/01/2023) in view of Pugia et al. (Pugia)(US20180284108)(See PTO-892 Notice of References Cited) and Rizzo et al. (Rizzo)(See PTO-892 Notice of References Cited).
See claims 2, 5-6, 12, 13 and 15 as submitted 09/01/2023.
Regarding claim 2, Rees teaches: “a method of determining the presence or absence of a target microorganism in a test sample, the method comprising…”(Abstract); a porous lateral flow strip (reference claim 4, p. 5); a sample pad (reads on a deposition zone); and an immobilization zone on or in said substrate with a capture element specific to the target microorganism with for example, bacteriophage (reference claim 19) (reads on phage fixation zone). Rees also teaches contacting a biological sample to the sample pad and eluting said sample through said strip so that the microorganism reaches the immobilization zone to form a phage-target microorganism complex.
Regarding claim 12, Rees teaches reference FIG. 3A-FIG. 3D, which shows an “immobilization” zone on which several capture elements (170), e.g., a bacteriophage, are fixed which is very similar to the depiction in instant application FIG. 2. And FIG 3.
Rees does not teach contacting a marker with said biological sample, or a phage exposing a peptide selective for a microorganism.
Regarding claims 2, 5 and 6, Pugia teaches a method of isolating and measuring variations in an analyte sample, said method comprising: (a) binding said analyte sample having variations to a particle having attached analytical labels; (b) separating the resulting particles from the sample; (c) removing the analytical labels from the particle; and (d) measuring the analyte molecules by the measuring analytical labels (as recited in reference claim 1). Pugia also teaches the method of reference claim 1, wherein particles binding variation of analyte are removed by a porous matrix, a capture particle, a cell or magnetic particle or combinations thereof (as recited in reference claim 18) as well as the method of claim 1, wherein analytical labels are detected by mass spectroscopy, fluorescence, chemiluminescence or optically labels or combinations thereof (as recited in reference claim 19).
The sample can be a biological sample [0112], and the analyte of interest, can be a “gram-positive bacteria… staphylococcus sp.”[0143]. The term “analytical label” refers to a chemical entity (organic or inorganic) which is capable of generating a signal detectable by optical, MS, or electrochemical means” [0034]. Pugia also teaches “electrochemical analytical labels refers to potentiometric, capacitive and redox active compounds such as: metals like Pt, Ag, Pd, Au and many others or; particles like gold sols, graphene oxides and many others or; electron transport molecules like ferrocene”[0062].
Pugia does not teach a phage exposing a peptide selective for a microorganism.
Regarding claims 2, 13, and 15, Rizzo, however, teaches a method for the rapid identification of S. epidermidis using a novel phage clone, 9IIIB5 exposing SWSCTRYAA amino acids (as recited in claims 2, 13, 15) sequence, exhibited the highest specificity of recognition (Fig. 2b) also towards other S. epidermidis strains (Section 3.2. Phage selection towards S. epidermidis, p. 5)(as recited in claim 14).
One of ordinary skill in the art would have been motivated to combine the method of determining the presence or absence of a target microorganism in a test sample using a porous lateral flow strip as taught by Rees, with a test sample containing a microorganism (Staphylococcus sp.)-marker (ferrocene) complex as taught by Pugia, and with a novel phage, exposing a peptide selective for the microorganism, S. epidermidis, e.g., the phage 9IIIB5 exposing SWSCTRYAA amino acids as taught by Rizzo as a capturing probe, in order to improve S. epidermidis detection, in specificity and speed, from a biological sample (See MPEP 2143, Rationale A. Combining prior art elements according to known methods to yield predictable results).
One of ordinary skill in the art would have had a reasonable expectation of success for combining the method of Rees, using a test sample consisting of a target microorganism (Staphylococcus sp.)-marker (ferrocene) complex, and employing the phage 9IIIB5 exposing SWSCTRYAA amino acids as taught by Rizzo. There would have been a reasonable expectation of success given the underlying materials and methods are known, successfully demonstrated in the context of phage biosensors, microbial detection, and point-of-care diagnostics, and commonly used as evidenced by the applied prior art.
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.
Claims 3, 14, and 16 are rejected under 35 U.S.C. 103 as being unpatentable over Rees (WO2006105504A1)(cited on IDS, 09/01/2023) in view of Rizzo et al. (Rizzo)(See PTO-892 Notice of References Cited).
See claims 3, 14 and 16 as submitted 09/01/2023.
Regarding claim 3, Rees teaches “[a] method of determining the presence or absence of a target microorganism in a test sample (as recited in instant claim 3 preamble), the method comprising…[Abstract, reference claim 1];
- flagging a bacteriophage (70) with a detectable flag (as recited in instant claim 3 “phage (4) being bound to a marker (5) to form a phage-marker complex (6))[Abstract, reference claim 1] (flag and marker are interpreted as interchangeable);
- combining flagged bacteriophage with the sample and providing conditions sufficient to allow flagged bacteriophage to attach to the microorganism creating a bacteriophage exposed sample (as recited in instant claim 3 “letting said phage (4) react with said biological samples (1) so as to allow, if said microorganism (2) is present, the binding of said phage (4) to said target microorganism (2) to obtain a sample comprising a microorganism-mark[er] phage complex (7)) [Abstract, reference claim 1];
- performing a target separation process, the process capable of separating the bacteriophage exposed sample into a target microorganism portion containing target microorganisms present in the sample and a portion containing flagged bacteriophage not bound to the target bacteria [Abstract, reference claim 1]…e.g., reference claim 12, wherein said washing comprises filtering said bacteriophage exposed sample through a filter that allows unbound phage to pass through while retaining the bound phage (as recited in instant claim 3 “filtering said sample comprising a microorganism-mark[er] phage complex (7);
- and assaying at least one of the portions to detect the presence or absence of the flag to determine the presence or absence of target microorganisms in the sample (as recited in instant claim 3 “detecting said microorganism-mark[er] phage complex (7)[Abstract, reference claim 1].
Rees does not teach a phage (4) exposing a peptide (3).
Regarding claims 3, 14 and 16, Rizzo, however, teaches a method for the rapid identification of S. epidermidis using a novel phage clone, 9IIIB5 exposing SWSCTRYAA amino acids (as recited in claims 3, 14, and 16) sequence, exhibited the highest specificity of recognition (Fig. 2b) also towards other S. epidermidis strains (Section 3.2. Phage selection towards S. epidermidis, p. 5)(as recited in claim 14).
One of ordinary skill in the art would have been motivated to combine the method of determining the presence or absence of a target microorganism in a test sample (combining said flagged bacteriophage with said sample; performing a target separation process, assaying at least one of said portions to detect the presence or absence of said flag to determine the presence or absence of said target microorganism in said sample) as taught by Rees with employing a novel phage, exposing a peptide selective for the microorganism, in this case, more specifically S. epidermidis, e.g., the phage 9IIIB5 exposing SWSCTRYAA amino acids as taught by Rizzo as a capturing probe, in order to improve the phage - bacteria capturing efficiency within the biological sample (See MPEP 2143, Rationale A. Combining prior art elements according to known methods to yield predictable results).
One of ordinary skill in the art would have had a reasonable expectation of success for combining the method of Rees and the phage 9IIIB5 exposing SWSCTRYAA amino acids as taught by Rizzo. There would have been a reasonable expectation of success given the underlying materials and methods are known, successfully demonstrated in the context of phage biosensors, microbial detection, and point-of-care diagnostics, and commonly used as evidenced by the applied prior art.
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.
Claims 7 and 11 are rejected under 35 U.S.C. 103 as being unpatentable over Rees in view of Rizzo, as applied to claims 3, 14, and 16 above, and further in view of Xu et al. (Xu)(See PTO-892 Notice of References Cited) and Pugia et al. (Pugia)(See PTO-892 Notice of References Cited).
See claims 7 and 11 as submitted 09/01/2023.
Rees and Rizzo teach claim 3 but do not teach electrochemical molecular system/electrochemical markers.
Regarding claims 7 and 11, Xu, however, reviews phage based electrochemical sensors and teaches “[p]hages based electrochemical sensors have received much attention due to their high specificity, sensitivity and simplicity. Phages or bacteriophages provide natural affinity to their host bacteria cells and can serve as the recognition element for electrochemical sensors. It can also act as a tool for bacterial infection and lysis followed by detection of the released cell contents, such as enzymes and ions (p.1, Abstract). Xu additionally teaches “[b]acteriophages can be used as recognition elements for target bacteria detection due to their natural ability to capture and lyse their host bacteria cells. Therefore, the bacteriophage functionalized electrochemical sensor can be used for detection of different bacteria strains in many different samples. In addition, except to act as a bio-receptor, bacteriophages could also be used to infect and lyse the bacteria cells, followed by detection of the release intracellular contents. Impedimetric and amperometric measurements are the most commonly employed detection techniques in the research works related to phage-based electrochemical biosensors (p. 7).
Xu does not teach specifically ferrocene.
Pugia, however, teaches ferrocene as an example of an electrochemical marker [0062].
One of ordinary skill in the art would have been motivated to substitute an electrochemical marker as taught by Xu, and particularly ferrocene, as taught by Pugia, as opposed to other options as taught by Rees, because of their high specificity (see Table 1, p. 11), sensitivity, simplicity, and in some cases, their low cost (See MPEP 2143, Rationale B. Simple substitution of one known element for another to obtain predictable results).
One of ordinary skill in the art would have had a reasonable expectation of success for substituting an electrochemical marker as taught by Xu and, and particularly ferrocene as taught by Pugia. There would have been a reasonable expectation of success given the underlying materials and methods are known, successfully demonstrated in the context of phage biosensors, microbial detection, and point-of-care diagnostics, and commonly used as evidenced by the applied prior art.
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.
Conclusion
No allowable claims.
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/C.C./Examiner, Art Unit 1672 /M FRANCO G SALVOZA/Primary Examiner, Art Unit 1672
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