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 .
The claims dated 7/3/2025 are under consideration.
The amendments and arguments presented in the papers filed 7/3/2025 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 1/3/2025 listed below have been reconsidered as indicated.
a) The objection to the drawings is withdrawn in view of the grayscale drawings submitted.
b) The objections of claims 4, 6, 8 and 9 are withdrawn in view of the amendments to the claims.
c) The rejections of 112(b) Claims 1-3, 5, 7 and 9-10 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph are withdrawn. However, the claims are rejected as necessitated by the amendments.
d) The rejections of claims 3, 5 and 7 under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, are withdrawn in view of the amendments to the claims.
e) The rejections of claims 1-10 under 35 U.S.C. 102(a)(1) as being anticipated by Crost (PLOS ONE. 2013. 8(10):e76341) are withdrawn in view of the amendments to the claims.
The Examiner’s responses to the Remarks regarding issues not listed above are detailed below in this Office action.
New and modified grounds of rejection necessitated by amendment are detailed below and this action is made FINAL.
Election/Restrictions
Applicant elected, with traverse of Group I, claims 1-10 in the reply filed on 8/2/2024.
Claims 13, 14, 15 and 16 are included with the election of Group I as they depend from claim 1.
Drawings
High resolution copies of the drawings may be accessed via PAIR/Patent Center Retrieval using the Supplemental Content tab.
Claim Objections
The following objection has been maintained.
Claim 10 is objected to because of the following informalities: the claims each recite “the transporter protein” rather than “the sialic acid transporter protein” as set forth in claim 1. It is suggested a single term consistently be used when referring to a particular claim element. Appropriate correction is required.
The following are new objections.
Claim 1 is objected to because of the following informalities: the claim states “wherein the DNA is analysed to detect the presence of at least part of the faecal biomarker sialic acid transporter protein specific to 2,7-anhydro-Neu5Ac of Ruminococcus gnavus (R. gnavus) ATCC 29149 Nan cluster gene RUMGNA 02698”. It is suggested the claim recites the “is analysed” language in the active voice rather than passively. For example, the claim may be amended to recite:
A method to detect at least part of a sialic acid transporter protein to identify, monitor and/or diagnose a mucosal bacterial presence or infection, the method comprising:
detecting a faecal biomarker by:
collecting a faecal sample;
extracting DNA from the faecal sample; and
detecting the presence of at least part of the faecal biomarker by analysing the extracted DNA,
wherein the faecal biomarker comprises Ruminococcus gnavus ATCC 29149 Nan cluster gene RUMGNA_02698.
Appropriate correction is required.
Claim 1 is objected to because of the following informalities: the claim states “the faecal biomarker sialic acid transporter protein specific to 2,7-anhydro-Neu5Ac of Ruminococcus gnavus (R. gnavus) ATCC 29149 Nan cluster gene RUMGNA 02698”. The phrase appears to be lacking a verb identifying the faecal biomarker as a “sialic acid transporter protein specific to 2,7-anhydro-Neu5Ac of Ruminococcus gnavus (R. gnavus) ATCC 29149 Nan cluster gene RUMGNA 02698”.
Appropriate correction is required.
Claims 14 and 15 are objected to because of the following informalities: the claims each recite “the transporter protein” rather than “the sialic acid transporter protein” as set forth in claim 1. It is suggested a single term consistently be used when referring to a particular claim element.
Appropriate correction is required.
Claim 16 is objected to because of the following informalities: the claims each recite “the substrate or solute binding protein” rather than “the sialic acid transporter protein” as set forth in claim 1. It is suggested a single term consistently be used when referring to a particular claim element.
Appropriate correction is required.
Claim Interpretation
Claim 1 is drawn to a “method to detect at least part of a sialic acid transporter protein to identify, monitor and/or diagnose a mucosal bacterial presence or infection”; however, the active method steps do not explicitly require identifying, monitoring and/or diagnosing mucosal bacterial presence or infection. MPEP 2111.02 states:
If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention's limitations, then the preamble is not considered a limitation and is of no significance to claim construction.
Accordingly, the claim language of “method to detect at least part of a sialic acid transporter protein to identify, monitor and/or diagnose a mucosal bacterial presence or infection” merely sets forth the intended use or purpose of the claimed methods, but does not limit the scope of the claims. The claims are given the broadest reasonable interpretation as requiring: detecting a faecal biomarker, which in turn requires collecting a faecal sample; and extracting DNA from the faecal sample.
The claim includes a “wherein” clause stating “the DNA is analysed to detect the presence of at least part of the faecal biomarker sialic acid transporter protein specific to 2,7-anhydro-Neu5Ac of Ruminococcus gnavus (R. gnavus) ATCC 29149 Nan cluster gene RUMGNA_02698”. The clause uses the passive voice to describe an intended use of the DNA extracted from a faecal sample. The clause is interpreted as not further limiting the scope of the claim.
The body of claim 1 is interpreted as setting forth all of the active method steps required by the claim. The active method steps are sufficient to accomplish the goal set forth in the preamble. See Remarks, p. 1.
Claim 4 describes an intended use of the sialic acid transporter protein, but does not require any additional active method steps or further limit the step of “detecting” as set forth in claim 1.
Claim 6 further describes an intended use of the sialic acid transporter protein, but does not require any additional active method steps or further limit the step of “detecting” as set forth in claim 1.
Claim 7 further describes a therapy of claim 6, but does not require any additional active method steps or further limit the step of “detecting” step as broadly set forth in claims 1 and 6.
Claim 8 further describes a polymerase chain reaction (PCR) is used to amplify the protein and identify the presence of the transporter protein, but does not require any additional active method steps or further limit the “detecting” step of claim 1.
Claim 9 further describes qPCR is used to identify the presence of the transporter protein, but does not require any additional active method steps or further limit the “detecting” step of claims 1 and 8.
Claim 10 further describes an intended use of the presence or absence of sialic acid transporter protein, but does not require any additional active method steps or further limit the step of “detecting” as broadly set forth in claim 1.
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, 4, 6, 7, 8, 9, 10 , 13, 14 15 and 16 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.
Regarding claim 1, the claim states the “faecal biomarker” is Ruminococcus gnavus (R. gnavus) ATCC 29149 Nan cluster gene RUMGNA_02698 corresponding to a “sialic acid transporter protein specific to 2,7-anhydro-Neu5Ac”. This description of the gene RUMGNA 02698 as a sialic acid transporter protein specific to 2,7-anhydro-Neu5Ac is not supported by the specification. The specification identifies RUMGNA 02698 or “RgSBP” as a “substrate or solute binding protein” (p. 4, 5, 11, 17 and 37).
Claims 4, 6, 7, 8, 9, 10 , 13, 14 15 and 16 depend from claim 1 and are rejected for the same reason.
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, 4, 6, 7, 8, 9, 10 , 13, 14 15 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.
The following rejections have been maintained. The Remarks did not address these rejections, other than to state the “claims are currently amended to clarify the invention” (p. 1).
Regarding claim 4, the claim states “transporter protein is used as an indicator or biomarker for inflammatory bowel disease”. It is unclear if the claim is setting forth an intended use of the method of claim 1, or if it requires a second active method step of detecting inflammatory bowel disease by using the transporter protein as an indicator or biomarker of inflammatory bowel disease.
Regarding claim 6, the claim states “the presence of the transporter protein is used as an indicator of likelihood of success of microbiome-targeted therapies”. It is unclear if the claim is setting forth an intended use of the method of claim 1, or if it requires a second active method step of detecting a likelihood of success of microbiome-targeted therapies by using the transporter protein as an indicator of likelihood of success of microbiome-targeted therapies.
Claim 7 depends from claim 6 and is rejected for the same reason.
Regarding claim 8, the claim refers to PCR being “used” to amplify the protein and identify the present of the sialic acid transporter protein. It is unclear how PCR is used to amplify or identify a “protein” as PCR amplifies nucleic acids.
It is further unclear if the claim is intended to further limit the “detecting” step of claim 1, or if it requires a second active method step of “using PCR” to identify the presence of the sialic acid transporter protein.
Claim 9 depends from claim 8 and is rejected for the same reason.
Regarding claim 10, the claim states “the presence or absence of the transporter protein is used to distinguish or diagnose Ulcerative Colitis or Crohn’s Disease”. It is unclear if the claim is setting forth an intended use of the method of claim 1, or if it requires a second active method step of distinguishing or diagnosing Ulcerative Colitis or Crohn’s Disease by using the presence or absence of the transporter protein.
The following are new rejections necessitated by the amendments to the claims.
Regarding claim 1, the claim includes a “wherein” clause stating “the DNA is analysed to detect the presence of at least part of the faecal biomarker sialic acid transporter protein specific to 2,7-anhydro-Neu5Ac of encoded by Ruminococcus gnavus (R. gnavus) ATCC 29149 Nan cluster gene RUMGNA 02698”. It is unclear if the clause is setting forth an intended use of the DNA extracted from the faecal sample or if the claim requires an active method step of “detecting the presence of at least part of the faecal biomarker by analysing the extracted DNA”.
Claims 4, 6, 7, 8, 9, 10, 13, 14, 15, and 16 depend from claim 1 and are rejected for the same reason.
Regarding claim 13, the claim recites “the bacterium” and the phrase lacks proper antecedent basis.
Regarding claim 14, the claim states “Typically” the transporter protein is encoded by ATCC 29149 Nan cluster. It is unclear if the transporter protein described by the claim by be encoded by genomic sequences other than the ATCC 29149 Nan cluster.
Regarding claim 16, the claim recites “the substrate or solute binding protein” and the phrase lacks proper antecedent basis.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 4, 6, 10 and 13-16 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
The following rejections have been maintained. The Remarks did not address these rejections, other than to state the “claims are currently amended to clarify the invention” (p. 1).
Regarding claim 4, the claim describes an intended use of the sialic acid transporter protein, but does not limit the scope of the “detecting” step of claim 1 or require any additional active method steps. Claim 4 fails to further limit claim 1.
Regarding claim 6, the claim describes an intended use of the presence of the sialic acid transporter protein, but does not limit the scope of the “detecting” step of claim 1 or require any additional active method steps. Claim 6 fails to further limit claim 1.
Regarding claim 10, the claim describes an intended use of the presence or absence of the sialic acid transporter protein, but does not limit the scope of the “detecting” step of claim 1 or require any additional active method steps. Claim 10 fails to further limit claim 1.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
The following are new rejections necessitated by the amendments to the claims.
Regarding claim 13, the claim specifies the bacterium is R. gnavus, identical to the bacterium specified in claim 1.
Regarding claim 14, the claim specifies the transporter protein is encoded by ATCC 29149 Nan cluster, identical the protein specified in claim 1.
Regarding claim 15, the claim specifies the transporter protein is specific to 2,7-anhydro-Neu5Ac, identical to the protein specified in claim 1.
Regarding claim 16, the claim specifies the protein is encoded by RUMGNA 02698, identical to the protein specified in claim 1.
In total claims 13-16 fail to include any additional elements not recited in claim 1 from which they depend.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1, 2, 4, 6, 7, 8, 9 and 10 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Sagheddu (Front Pediatr. 2016. 4:57, 6 pages).
Regarding claim 1, Sagheddu teaches collecting a faecal sample (p. 2, Subjects). Sagheddu teaches extracting DNA from the faecal sample (p. 2, Fecal DNA Extraction).
These two steps taught by Sagheddu are sufficient to accomplish “detecting a faecal biomarker” because the claim defines the step of “detecting a faecal biomarker” is done “by” performing these two steps.
The “wherein” clause is broadly interpreted as setting forth in the passive voice the intended use of the DNA, and does not limit the scope of the claims.
The active method steps set forth as interpreted above are sufficient to accomplish the goal set forth in the preamble of the claim. No active method steps of detecting at least part of a sialic acid transporter protein, identifying a mucosal bacterial presence or infection, monitoring a mucosal bacterial presence or infection or diagnosing a mucosal bacterial presence or infection are required.
Regarding claim 2, the claim recites a property inherent to the sialic acid transporter gene regarding its use as an indicator or biomarker. It is further noted that such a property does not need to be recognized by the prior art at the time of filing.
Regarding claim 4, the claim does not require any additional elements beyond that of claim 1. Claim 4 is anticipated for the same reason as claim 1.
Regarding claims 6 and 7, the claim does not require any additional elements beyond that of claim 1. Claims 6 and 7 are anticipated for the same reason as claim 1.
Regarding claims 8 and 9, the claim further limits the intended use of the claim 1 as recited in the “wherein” clause.
Sagheddu anticipates claims 8 and 9 because it teaches all of the active method steps as set forth by the claim.
Regarding claim 10, the claim does not require any additional elements beyond that of claim 1. Claim 10 is anticipated for the same reason as claim 1.
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.
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.
Claim(s) 1, 4, 6, 7, 8, 9, 10, 13, 14, 15 and 16 is/are rejected under 35 U.S.C. 103 as being unpatentable over Sagheddu (Front Pediatr. 2016. 4:57, 6 pages) in view of Crost (Gut Microbes. 2016. 7(4):302-312).
The following rejections are over embodiments in which the RUMGNA 02698 gene is detected in DNA extracted from a faecal sample.
Regarding claims 1, 8, 9, 13, 14, 15 and 16, Sagheddu teaches collecting a faecal sample (p. 2, Subjects). Sagheddu teaches extracting DNA from the faecal sample (p. 2, Fecal DNA Extraction).
Sagheddu further teaches the use of PCR assays to examine extracted DNA (p. 2, PCR-DGGE and Quantitative PCR), including detecting R. gnavus (Table 1).
While Sagheddu teaches the above methods, Sagheddu does not specifically teach the analysis of RUMGNA 02698.
However, Crost teaches that R. gnavus ATCC 29149 and ATCC 35913 engage in the use of mucins for growth (Abstract). The genes for this process are encoded by a Nan cluster (p. 307). The genes encoded are different and include: RUMGNA_02698 in ATCC 29149 and RGNV35913-01296 in ATCC 35913 (Fig. 5).
It would have been prima facie obvious to the ordinary artisan to have modified the method of Sagheddu to have used PCR to further evaluate the faecal samples of Sagheddu for the presence of Nan cluster genes including RUMGNA_02698 in ATCC 29149. One would have been motivated to analyze this to determine whether or not the R. gnavus detected is able to grown on mucin. One would have an interest in growth on mucin because it provides R. gnavus a competitive nutritional advantage, allowing the bacteria to thrive within mucosal environments by scavenging sialic acid from host mucus in a form, 2,7-anhydro-Neu5Ac, that can be used to their own benefit (p. 310 of Crost).
Regarding claim 4, the claim does not require any additional elements beyond that of claim 1. Claim 4 is rendered obvious for the same reason as claim 1.
Regarding claims 6 and 7, the claim does not require any additional elements beyond that of claim 1. Claims 6 and 7 are rendered obvious for the same reason as claim 1.
Regarding claim 10, the claim does not require any additional elements beyond that of claim 1. Claim 10 is rendered obvious for the same reason as claim 1.
Conclusion
No claims 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 JOSEPH G DAUNER whose telephone number is (571)270-3574. The examiner can normally be reached 7 am EST to 4:30 EST with second Fridays Off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached at 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JOSEPH G. DAUNER/Primary Examiner, Art Unit 1682